CasaXPS Manual 2.3.15 Rev 1.0

Copyright © 2010 Casa Software Ltd

CasaXPS Manual 2.3.15
CasaXPS Processing Software
Casa Software Ltd.

NO WARRANTY
Casa Software Ltd. does its best to ensure the accuracy and reliability of the Software andRelated Documentation. Nevertheless, the Software and Related Documentation may
contain errors that may affect its performance to a greater or lesser degree. Therefore no
representation is made nor warranty given that the Software and Related Documentation
will be suitable for any particular purpose, or that data or results produced by the
Software and Related Documentation will be suitable for use under any specificconditions, or that the Software and Related Documentation will not contain errors. Casa
Software Ltd. shall not in any way be liable for any loss consequential, either directly or
indirectly, upon the existence of errors in the Software and Related Documentation. The
Software and Related Documentation, including instructions for its use, is provided “AS IS”
without warranty of any kind. Casa Software Ltd. further disclaims all implied warranties
including without limitation any implied warranties of merchantability or fitness for aparticular purpose. CasaXPS should not be relied on for solving a problem whose incorrect
solution could result in injury to a person or loss of property. The entire risk arising out of
the use or performance of the Software and Related Documentation remains with the
Recipient. In no event shall Casa Software Ltd. be liable for any damages whatsoever,including without limitation, damages for loss of business profit, business interruption,
loss of business information or other pecuniary loss, arising out of the use or inability to
use the Software or written material, even if Casa Software Ltd. has been advised of thepossibility of such damages.

Acknowledgements
Casa Software Ltd would like to thank all those providing data and offering
enlightening discussions leading to the current state of the CasaXPS softwareand manual. It is a humbling experience to work with so many knowledgeable
people and the author would like to express gratitude to all concerned.

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Contents
CasaXPS Processing Software ............................................................................................................ 1
Casa Software Ltd. ........................................................................................................................... 1
NO WARRANTY ............................................................................................................................... 1
Acknowledgements ............................................................................................................................. 1
The Nature of ToF Spectra................................................................................................................... 5ToF Mass Calibration ........................................................................................................................... 7
Calibration Based on Nominal Masses ............................................................................................ 9
An Example of Mass Calibration using Nominal Masses ........................................................... 11
Recalibration of Mass Scale for ToF Spectra ..................................................................................... 15
Recalibration Steps ........................................................................................................................ 17
Peak Fitting ToF SIMS Data ................................................................................................................ 18
Line-shapes Suitable for ToF SIMS Spectra ................................................................................... 19
Peak Identification and Reduction .................................................................................................... 21
IonToF Peak Identification ................................................................................................................. 23
Converting IonToF Spectra................................................................................................... 24

Directory Profiling ......................................................................................................................... 26
Profile Directory Toolbar Option...................................................................................... 28

Working with ToF Spectra in CasaXPS ............................................................................................... 29
Time to Mass Calibration Procedures ........................................................................................... 29
Mass Calibration using Regions and Propagation of Regions between Spectra ....................... 30
Mass Calibration ........................................................................................................................ 31
Propagation of Calibration Regions ........................................................................................... 31
Mass Calibration using the Exact Mass Calculator Property Page: ........................................... 33
The Element Library from a ToF Perspective ................................................................................ 35
The Element Library and Linking ToF Peaks for Display ............................................................ 36
Profiling Features for ToF data .......................................................................................................... 47
ToF Data File Options .................................................................................................................... 49
Create a Total Ion Spectrum............................................................................................. 50

Create Images from Spectra using Quantification Regions ....................................................... 52
Spectra Generated from Image Zones ...................................................................................... 54
Creating a Profile from a Total Ion Spectrum ............................................................................ 56
Spectra Generated from Profile Layers............................................................................. 582

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Create a Profile from a Directory of Files.......................................................................... 58

Convert and Merge a Directory of XYT File....................................................................... 61

Image Depth Profile Data Analysis.............................................................................. 63

Quantification Reports and ToF Data................................................................................................ 66
Quantification via the Report Spec Property Page ....................................................................... 66
Standard Report ........................................................................................................................ 67
Custom Report .......................................................................................................................... 70
An Overview of Working with ToF Data in CasaXPS ......................................................................... 72
SIMS Toolbar Buttons: Display Options ........................................................................................ 72
An Overview .................................................................................................................................. 79
Basics of CasaXPS .......................................................................................................................... 81
Converting Data ........................................................................................................................ 81
Data Viewed Via an Experiment Frame .................................................................................... 82
Displaying Data.......................................................................................................................... 83
Selecting VAMAS Blocks ............................................................................................................ 84
Tile Display Options ................................................................................................................... 85
Display Colours .......................................................................................................................... 86
Calculating SNMS Sensitivity Factors ............................................................................................ 88
Quantification of SNMS Profiles.................................................................................................... 98
Quantification of Stainless Steel using SNMS: an Example ....................................................... 98
Specifying the Sputter-Rate .................................................................................................... 103
Creating a Calibrated SNMS Profile......................................................................................... 104
Dynamic SIMS.................................................................................................................................. 109
Notes on Dynamic SIMS RSF Calculation .................................................................................... 110
Reference Signal Measured during the Course of Profile ....................................................... 110
Reference Signal Measured at End of Acquisition Cycles ....................................................... 111
Quantification of Dynamic SIMS Profiles .................................................................................... 112
Quantification of Basic Profiles ............................................................................................... 114
Making Adjustments to the Sputter Rate ............................................................................... 125
Display of Calibrated Profiles .................................................................................................. 126
Further Aspects of Dynamic SIMS Quantification ....................................................................... 127
Logical Structure of a SIMS Depth Profile within CasaXPS ...................................................... 127
Methods for Computation of RSF and Sputter Rate Values ................................................... 128
Identification of the Matrix and Interface Cycles.................................................................... 128

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Selecting Ranges of Cycles on the Calibration Property Page ................................................. 132
Surface Data and Background Signal ....................................................................................... 133
Three Ways to Calculate RSF Values from Standard Samples ................................................. 134
Adding RSF and Sputter Rates to Profile Data ......................................................................... 135
Applying Calibration Parameters to One or More Profiles...................................................... 135
Depth Profile Statistics: Areal Density and Decay Length ....................................................... 136
Maintaining Standards Library Files ........................................................................................ 137
Step-by-Step Description of Quantification for a Multi-Layer Sample.................................... 137
An Example of Computing an RSF using Dose and Implant Peak Depth ................................. 143
Computing RSFs where the Matrix Signal is Measured following the Completion of the Implant
Profile ...................................................................................................................................... 145
Gathering Profile Data for Display and Calibration Purposes ..................................................... 147

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TOF SIMSThe Nature of ToF Spectra
Time-of-Flight Mass Spectrometry (ToF MS) is based on the principle that ionscreated from a sample are accelerated into a flight tube using an electric
extraction field resulting in each ion of a given charge acquiring acharacteristic energy from a tight distribution of possible energies. Since thekinetic energy of the ions are nearly identical, the velocity attained by ionswith differing mass must also differ, thus the time taken for an ion with agiven charge to travel a given distance down the flight tube to the detector
discriminates between ions of different mass. Specifically, the mass of an ion
is proportional to the square of the time taken to travel a fixed distance.
Thus, ToF MS works on the basis of a stop-watch; a start event occurs as theextraction voltage is pulsed, followed by a sequence of stop events
representing the arrival of ions at the detector. To process a ToF mass
spectrum from the raw timing data, a histogram is created from the set oftime values, where the time events recorded during an experiment arecounted into time-bins. The relationship between the time events and themass of the ions responsible for the time events allows the time-bin
histogram to be viewed using a mass scale.
CasaXPS displays the ToF intensities with respect to the time bin indices, evenwhen a mass calibration is available. Converting a spectrum to mass binned
intensities involves a mapping which cannot be reversed; explicit steps must
be taken to perform the transformation between time and mass.
The following two plots are for the same data, both viewed in the time
domain. The mass range in these two plots is identical.

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The same spectrum plotted using a linear mass step size changes theperspective of the data as follows.

Spectra from ToF instruments traditionally appear as a single spectrum over awide range of mass. The spectral display reflects the parallel nature of thetechnique in the sense that counts are allocated over the entire range of timebins for each pulse of the ion gun. This is in contrast to quadrupole ormagnetic sector MS instruments where the signal is only recorded one mass
bin at a time. Nevertheless, for high resolution ToF MS the majority of timebins, particularly at low mass, contain little information, therefore CasaXPS
offers a means of converting ToF spectra from a single monolithic data set
into a set of mass intervals representative of the useful information content.
Each nominal mass, based on the current time to mass calibration, is isolated
into individual VAMAS blocks. Presenting a ToF spectrum as a set of many
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VAMAS blocks favours the tools within CasaXPS providing the basis for datacomparison and peak analysis via synthetic peak models.

The partitioning of the time bins into suitable mass ranges around thenominal masses requires a calibration for the mass scale.

ToF Mass Calibration
The relationship between the mass m of an ion and the time taken for the ionof a given charge to travel a fixed distance is quadratic in the flight time t. For
an ideal system, the time-to-mass relationship is:m [(t t 0 ) / b]2

where t0 represents a time offset and b scales the time values appropriately.
Since knowledge of these two parameters t0 and b is sufficient to describe
the relationship between the mass and time-of-flight, given two mass/timepairs the calibration parameters can be determined from a pair ofsimultaneous equations. In reality, assigning the mass/time coordinates fromthe time-binned spectra is not exact and therefore the time-to-mass
calibration must be computed in a least-squares sense using multiple
mass/time pairs. Further, the choice of mass/time pairs must be carefully
made to ensure accuracy of the calibration for both interpolated andextrapolated mass regions. Those mass regions falling within (interpolation)
the set of mass/time pairs used to create the calibration will be moreaccurate with respect to the time-to-mass calibration than those outside(extrapolation) the interval containing the mass/time pairs included in the7CasaXPS Manual 2.3.15 Rev 1.0

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least squares fit. It is therefore important to calibrate a spectrum using peaks
over as wide a mass range as possible and check that peaks, once calibrated,can be sequentially assigned to nominal masses. The following describes thetools in CasaXPS for calibrating a spectrum of time-bins with respect to massand how to assess the success of this procedure.

Figure 1

Figure 2: An example of a poor mass calibration based on extrapolation.

When calibrating the mass scale, the primary objective is to assign each
visible peak to a nominal mass. For some spectra and instruments, there may
be perfectly good reasons why this objective may fail, but in general eachpeak in the data should be associated with a nominal mass; any mass defectfrom the nominal mass provides information about the atomic or molecular
ion responsible for the peak. It is not necessary nor is it always possible toattribute each peak to a known ion, however, when properly calibrated, if theobservable peaks deviate from the sequence of nominal masses then theaccuracy of the calibration may be in doubt. The problem of calibrating themass scale reduces to identifying a set of peaks sufficiently well distributed
over the mass scale to provide plausible mass assignments for each and every
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peak in the spectrum. Figure 1 is an example of a mass calibration in which
the set of peaks displayed matches well with the computed mass positions;however the calibration is performed using only those peaks within thewindow in Figure 1 and a similar agreement, when using the same
calibration, for the molecules shown in Figure 2 is not achieved. The poor
mass calibration is remedied by simply including at least one of the peaks in
Figure 2 as part of the calibration set. The concept of progressively adding
calibration points to the set used to mass calibrate a spectrum is developed
in following sections.

Calibration Based on Nominal Masses

Figure 3: Nominal mass calibration

The procedure for calibrating a spectrum can be summarised as follows:
following an initial assignment based on at least two peaks, new peaks areprogressively added to the set of mass/time pairs until the observed peaks
are sequentially associated with nominal masses. The spectrum in Figure 3 iscalibrated based on nominal masses and an iterative improvement
procedure. This process can be performed manually using the Exact Massproperty page (Figure 4), where peaks are associated with formulae using themouse, or alternatively nominal masses are used in a sequence of steps
involving repeatedly:
1. Finding the peaks using the Find Peaks button.
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2. Replacing the current calibration list by nominal masses and times
determined from the regions obtained from the Find Peak operation.
The Load Regions button transfers the required information from thecurrent set of regions to the calibration list on the Exact Mass property
page.
3. Recalibrate the mass scale by pressing the Calib C,t0 button.

Figure 4: Exact Mass Calculator Property Page.

The Find Peaks button uses a threshold to identify peak structures in thedata; then for each peak identified, a region is created on the spectrum using
the name derived from the nominal mass determined from the region. The
Load Regions button transfers those nominal mass names and computed
positions to the calibration table on the Exact Mass property page for which
the computed mass is within a tolerance of the nominal mass. The search forthese acceptable mass/time pairs begins with the low masses, so the initial
calibration should begin with small masses, but typically greater than 10 amu.
With each repetition of these steps, the number of regions loaded into thecalibration table should increase until, ideally, all the peaks found areincluded in the calibration table. At this point, the spectrum so calibrated
should be surveyed to ensure the peaks, both minor and major, areassociated with the nominal masses on the abscissa scale.

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Figure 5: Raw time-binned spectrum.

Calibration using nominal mass values is not always appropriate, for example
heavy molecular ions; however, for some spectra, calibration using exact
masses is equally inappropriate. The data in Figure 1 is an example of aspectrum for which it is beneficial to use nominal masses rather than exact
masses; the spectrum derives from a total ion list file containing image
information and minor variations in acquisition conditions across the imaged
surface cause small shifts in the underlying peaks summed to form the total
ion spectrum. Peaks are neither high enough in mass resolution nor wellenough defined in terms of position to use an exact mass position. The lattercan be demonstrated using false colour images to extract spectra fromdifferent zones on the image.
An Example of Mass Calibration using Nominal Masses
Initially the spectrum is without a mass calibration as seen in Figure 5. The
first step is to identify two peaks.

Figure 6: Two peaks are identified by creating quantification regions.

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The regions defined on the spectrum in Figure 6 represent the initial pair ofmass/time coordinates used to produce a rough calibration for the massscale. The regions are created using the Regions property page on the
Quantification Parameters dialog window. Each region calculates the timebin representative of the peak, while the mass corresponding to thecomputed time-bin is entered into the name field of the quantification
region. In this case, the name fields are entered with the nominal masses 15
and 23, although these values could equally well have been entered using theformulae C+H*3 and Na, respectively. Calibration based on these two regions
is performed by pressing thetoolbar button. When the toolbar button ispressed, any spectra appearing in the Active Tile will be calibrated based onregions so defined on the displayed spectra.

Figure 7: Spectrum after initial mass calibration.

While the calibration in Figure 7 looks reasonable for masses close to thecalibration points, the high mass peaks are poorly calibrated. The largest
peak in Figure 8 differs by about 18 amu from the mass calibration shown in
Figure 3.

Figure 8: Poor mass calibration for high mass peaks. Same peaks as those displayed using theinset tile in Figure 3.

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While the initial mass calibration based to only two low mass peaks is clearlya problem at higher masses, the accuracy is sufficient to begin the iterative
process of build a fuller set of mass calibration points.

Figure 9: Exact Mass property page.

Figure 10: Result of Find Peaks with a threshold of 20.

Given the initial mass calibration based on the peaks labelled 15 and 23, theFind Peaks button on the Exact Mass property page shown in Figure 9 can beused to assign nominal masses to all peaks characterized by a thresholdvalue. On pressing the Find Peaks button, a dialog window appears in which athreshold value can be entered. In the case of the results shown in Figure 10
the threshold value was set to 20. Once a new set of regions are createdusing the Find Peaks button, the Load Regions button is pressed, theconsequence of which is the mass calibration table on the Exact Massproperty page is loaded with the set of calibration points determined fromthe regions currently defined on the spectrum, subject to the condition thatthe mass determined from the time bin for each region is within a toleranceof the nominal mass entered into the name field of the region. Following the13CasaXPS Manual 2.3.15 Rev 1.0

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initial mass calibration and application of the Find Peaks button, the set of
regions generated by the Find Peaks button in Figure 10 are limited by the
Load Regions button to those displayed in Figure 9. That is, all regions above
nominal mass 31 were sufficiently different from the nominal mass to be
rejected. The deviation of the computed mass for peaks above 31 amu fromthe nominal mass is a measure of the error in the original mass calibration.
Given the new set of calibration points, the Calib button on the Exact Massproperty page can be pressed resulting in an improved mass calibration.
Repeating the Find Peaks operation followed by reloading the regions into
the calibration table reveals that peaks up to 53 amu are now included in thecalibration table. A third iteration of these steps produced a calibration table
including peaks up to 228 amu, while a forth iteration extends the calibrationtable up to 561 amu, exhausting the set of peaks found using the Find Peaks
button. The mass calibration based on nominal masses is now complete. All
that remains is to verify the mass calibration by stepping through the spectral
peaks to confirm the presence of peaks at each amu and that known peaks
are correctly assigned.

Figure 11: High resolution ToF peaks clearly distinct from the nominal mass of 28 amu.

The procedure is not without flaw, so verification is necessary, but can
provide a means of improving an initial calibration with minimal effort. For
high resolution ToF spectra, the use of nominal masses will lead to a roughmass scale which requires refinement using resolved peaks and exact mass
formulae (Figure 11).
NB: The peak marker in Figure 11 for elemental Si is positioned to the lefthand side of the peak. When a ToF spectrum is calibrated using the option on
the toolbar, the position of peaks with respect to time are determined fromthe regions. While the peak maximum may appear to be a good choice for14

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the peak position, the asymmetry typically observed in ToF peaks and thevariety of peak shapes over a spectrum suggest, in general, the peakmaximum is less well defined than the leading edge of a peak. For thisreason, the position of the peak used for the calibration procedure is taken to
be the lower full width half maximum. Hence the peak markers will align withthe leading edge of the peaks rather than the peak maxima. Note that thecalibration option on the Exact Mass property page offers the choice of peak
position to the user without limitation.

Recalibration of Mass Scale for ToF Spectra
Occasionally ToF Spectra are supplied as mass binned data. While data inmass bins is convenient for those without the ability to handle the relatively
large time binned spectra, the possibility exists that the mass calibration used
to mass-bin the spectra may not be accurate enough for the application inquestion. For high resolution mass spectra, a small error in the original timeto-mass calibration may lead to the type of uncertainty illustrated in Figure
12, where the peak maximum falls between the two most likely assignments
for the measured data. A recalibration of the mass bins is therefore required.

Figure 12: An example of a mass-binned spectrum where the original mass calibration is not
sufficiently accurate for the resolution of the peak shown.

The recalibration of mass-binned data differs from a time-to-mass calibrationof time-binned data in that the act of reallocating the counts to mass-binsfrom the original time-binned data (performed during the creation of themass spectrum), results in the loss of information. Namely, two or moretime-bins may map into the same mass-bin, therefore it is impossible to takea mass-bin and repopulate the time-bins with the same distribution found in
the original data set. The consequence of there being a fundamental
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difference between these two operations is that, when recalibrating a massbinned spectrum, the functional form used to assign the data bins to mass
values must involve a general three parameter quadratic function rather than
the stiffer model used to calibrate time-bins to mass-bins. The two parameter
calibration function recommended for time-to-mass calibration is too specificto the counting mechanism used to acquire the ToF MS data. The extra
flexibility offered by the three parameter quadratic is needed to model theerrors in the original time-to-mass calibration; the stiffer two-parameter
quadratic model used for time-to-mass calibration is dictated by andappropriate to the physics of the ToF instrument.
While CasaXPS allows time-to-mass calibration using both the recommended
two-parameter quadratic model and the general three-parameter quadratic
function, the same warning about the three-parameter functional form isequally applicable to both situations. That is, the flexibility offered by thegeneral quadratic function allows non-physical solutions for the mass
assignment of peaks. It is possible to create a mass calibration when using
the three-parameter quadratic for which known peaks are apparently
correctly assigned to masses, yet other peaks in the spectrum are incorrectly
assigned. Extrapolation based on the three parameter model should beviewed with suspicion. Ideally, ToF MS data should be provided in the time
domain, nevertheless situations do occur where mass-binned data must be
managed and therefore CasaXPS provides a mean of recalibrating the massbinned data. Figure 13 shows the same data seen in Figure 12 following therecalibration procedure described below.

Figure 13: The same mass spectrum after recalibration.

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Recalibration Steps
1. Cancel the Mass calibrated status of the spectra: overlay the massbinned spectra in the Active Tile and press thetoolbar button on
the SIMS toolbar. The label for the abscissa will return to “Time Bin”,
which indicates the data is in a state where a new calibration can becreated. Note, the abscissa values will be bin indices, not true timebins, but nevertheless it is necessary to the calibration procedure thatthe abscissa label is assigned the string “Time Bin”.
2. Using the Exact Mass Calculator, a new calibration set defining therelationship between the peaks and the mass assignment must be
established. The procedure is identical to creating a time-to-mass
calibration described elsewhere.
3. Perform the recalibration using the
button on the Exact Mass
Calculator property page of the Element Library dialog window.

Figure 14: A mass-binned peak illustrating the peak deformations due to the re-binningalgorithm used to create the mass spectrum.

An alternative procedure is to create quantification regions and apply therecalibration using thetoolbar button. While possible, this approach
suffers from the information lost during the time-to-mass conversion
procedure, that is, the mass-bins for higher mass values tend to be poorly
defined compared to the original time data (Figure 14). The algorithms for
identifying a peak position and therefore determining the calibration points
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assumes the data obeys Passion statistics, but otherwise varies smoothly; it isclear from Figure 14 that the mass-binned data contains anomalous values.

Peak Fitting ToF SIMS Data
The features in CasaXPS typically used to model XPS data envelopes can also
be used to analyst overlapping peaks in high resolution ToF SIMS spectra. The
principal difference between ToF SIMS and XPS is that asymmetry in ToF
SIMS peaks is, in general, in the opposite direction to that found for XPS
peaks. As a result, not all line-shapes in CasaXPS are appropriate for ToF SIMS
peaks, however the more recently introduced asymmetric line-shapes of LA
and LF provide a means of creating line-shapes appropriate for the range of
ToF SIMS peaks observed in practice.
The data in Figure 15 illustrates the similarities between XPS and ToF SIMS,
where the mass peaks associates with a nominal mass of 42 are very typicalof polymer XPS spectra such as PMMA or PET. The problems ofunderstanding the data are also similar in that both the position and theintensity of the underlying peaks are of importance when identifying themolecular ions responsible for the measured data.

Figure 15: Example of ToF SIMS peak structure.

The procedure for adding synthetic components to the data involves firstadding a quantification region to the data with background type set of “Zero”
before adding synthetic line-shapes. Creating and adjusting regions andcomponents is performed on the Quantification Parameters dialog window
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available from the Quantify option on the Options menu or the
toolbarbutton on the top toolbar of CasaXPS. Regions and components are managed
using the tables found on the Regions and Components property pages of
the Quantification Parameters dialog window shown in Figure 16.
The peaks shown in Figure 15 are defined using the parameters displayed in
the table on the Components property page illustrated in Figure 16. The lineshape parameter in this example is defined using the LA functional form,
where the parameters provide a degree of asymmetry to the right of thepeak maximum. The meaning of these parameters is described below.

Figure 16: Quantification Dialog Window.

Line-shapes Suitable for ToF SIMS Spectra
The success of a peak fit is dependent on an appropriate choice for the lineshape parameter. As stated above, the LA and LF line-shapes offer sufficient
flexibility for most ToF SIMS peak shapes.
The Lorentzian line-shape with FWHM F and position M is given by
L ( x : f , e)

1
x e
1 4
f

2

(1)

The functional form is symmetrical about x = M. In order to retain thecharacteristics of the Lorentzian line-shape and yet also introduce
asymmetry, the LA line-shape is defined in two halves as19

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Copyright © 2010 Casa Software Ltd(2)LA(α,β,m): Equation (2) defines the first two parameters used in the lineshape LA(α,β,m) shown in Figure 16. The third parameter m is used tocontrol the width of a Gaussian convolution applied to the functional form
defined by Equation (2). As a consequence of the definition for the LA lineshape, an asymmetry line-shape is established by specifying α not equal to β.
Further, is α is greater than β then the resulting peak will be asymmetric withan extended tail to the right of the peak maximum. Adjusting the Gaussianconvolution parameter causes the extent of the asymmetric tail to reduceand also shifts the peak maximum towards the extended tail.
LF(α, β, w, m): Identical to the LA line-shape with the exception that the
specified values of α and β are force to increase to a constant value via asmooth function determined by the width parameter w. The w parameter isused to restrict the extent of the tail.

Figure 17: Asymmetric Mass Peak fitted using a single LA line-shape.

By way of example, the elemental sodium mass peak shown in Figure 17
exhibits significant asymmetry to the right of the peak maximum, which canbe modelled using the LA line-shape. Note that the line-shape included in the
annotation of the peak in Figure 17 is achieved by setting the first parameterto a value greater than unity, thus compressing the tail to the left compared20

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to the tail to the right. Further, the Lorentzian tail to the right of the peakmaximum is adjusted by convoluting the functional shape with a Gaussian ofcharacteristic width described by a value of 250 for the m parameter in the
LA definition. The degree of asymmetry is determine by the relative size ofthe first parameter compared to the second, that is α > β.

Figure 18

The line-shape used in Figure 17 should be compared with the line-shape in
Figure 18 corresponding to a similar sodium peak measured using the same
IonToF instrument but using a different ion gun. The peak in Figure 18 rises
more quickly than the peak in Figure 17, therefore the α-parameter is now
much larger than the β-parameter, which is also set to a value greater thanunity. The larger the values for these two parameters the steeper the edge ofthe peak appears. Also note in Figure 18 that the Gaussian convolution ismuch narrower than that used in Figure 17. Possible values for the Gaussian
parameter are between 0 and 499; m = 0 corresponds to no convolution
being performed.

Peak Identification and Reduction
High resolution ToF spectra typically consist of numerous peaks, however forsome analyses only a small number of correlated peaks are significant for21

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distinguishing between samples. That is, a peak at one mass is only
characteristic of a particular compound when also accompanied by peaks at a
set of very specific masses. Given the plethora of peaks typically present in
ToF MS data, a means of grouping and displaying only significant peaks isrequired. To visualise the spectrum with respect to only significant peaks, a
ToF spectrum can be organised in CasaXPS 2.3.15 such that the Element
Library property page simplifies the mechanism by which these significant
peaks can be displayed for visual inspection. In addition to the element
marks, a spectrum can be broken into an array of VAMAS blocks representing
the peak information associated with the nominal masses and the element
library used to display appropriate subsets of these VAMAS blocks forinterpretation.
The procedure for splitting a ToF spectrum into a set of mass calibrated
VAMAS blocks can be performed using the toolbar button indicated in Figure
19. As an alternative approach, for data files for which a mass calibration isavailable to CasaXPS at the time of conversion the division of the data into
mass calibrated VAMAS blocks can be performed at the time the data areconverted. Either route to the mass calibrated VAMAS blocks requires a mass
calibration for the data.

Figure 19: ToF Spectrum with data in time domain.

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The data in Figure 19 are converted to a mass calibrated set of VAMAS blocks
by pressing thetoolbar button with hint Split into Unit Mass Spectra. The
result of converting the data in Figure 19 is shown in Figure 20, where theright-hand pane displays the set of VAMAS blocks derived from the single
VAMAS block in Figure 19.
The display in Figure 20 is achieved by overlaying the full set of VAMAS blocks
from the right-hand pane in the active tile. An inset tile is used to display a
specific VAMAS block, namely the VAMAS block corresponding to a nominal
mass of 42. Note that since the individual VAMAS blocks are mass calibrated,the overlay appears in the form of a mass calibrated spectrum.

Figure 20: ToF Spectrum after conversion to mass calibrated VAMAS blocks.

The discussion that follows relates to data prepared in the format shown in
Figure 20. Presenting the spectrum as a set of VAMAS block provides thebasis for the tools within CasaXPS. Before describing these tools, the method
for converting data files directly to mass calibrated sets of VAMAS blocks will
be addressed. Version 2.3.15 of CasaXPS only offers data conversion to themultiple VAMAS block format for ASCII files formatted using the convention
adopted by the IonToF data system.

IonToF Peak Identification
IonToF spectra are exported in ASCII files in the format shown in Figure 21.
The follow describes the options in CasaXPS for importing these data informats suitable for compiling peak lists.

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Figure 21:IonToF ASCII format.

The SIMS toolbar in CasaXPS offers two toolbar buttons for controlling theimport of data in the format shown in Figure 21. These toolbar buttons areindicated in Figure 22.
Figure 22: SIMS Toolbar buttons

The traditional method for working with ToF data is based on a single data
block approach, however the tools for peak identification now added to
CasaXPS are organized on a partitioning of the data into numerous data
blocks based on the nominal mass for each group of peaks. The objective is toanalyze a directory of spectra and determine a set of mass peaks andintensities for each spectrum in the directory.

Converting IonToF Spectra

Figure 23: ASCII txt files exported from the IonToF software.

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A data directory initially contains a set of spectra exported from the IonToF
software as ASCII txt files. Figure 23 illustrates such a directory which isdisplayed using the File Dialog window offered by the
toolbar button. The
conversion of these data may be performed using several filter strings asfollows:
1. “.ion”
2. “.amu”
3. “.sum”.
To initiate a conversion sequence, a name followed by one of the above
strings must be entered into the File name text-field on the File Dialog in
Figure 23. For example, to convert and merge the set of txt files in a format
suitable for peak identification, the File name text-field should be enteredwith the string “datafile.amu”. The base-name is arbitrary, however theextension “.amu” instructs the set of txt files to be converted to VAMAS
format (a new VAMAS file will appear in the directory for each txt fileprocessed) then these converted files are merged into a single experimentframe in CasaXPS. Note that these data are large; therefore the process isboth time consuming and requires plenty of PC memory!
The different filter strings determine the nature of the data files generated
from the IonToF ASCII files. The individual VAMAS files generated from the
ASCII files are identical for both the “.amu” and “.sum” filters; the final
outcome differs however, where the “.amu” filter causes the merger of thespectra into a single experiment frame as separate spectra equivalent to theoriginal ASCII data, while the “.sum” filter results in the total counts from theset of spectra in the ASCII files forming the equivalent of a single mass
spectrum. In both cases, the mass spectrum from each of the IonToF files ispartitioned into VAMAS blocks corresponding to data in the vicinity of thenominal mass values. Figure 24 shows the result of using the “.sum” filter on
the data directory depicted in Figure 23. Both display tiles in Figure 24 display
an overlay of all the data blocks in the right-hand pane of the experimentframe and the inset tile shows the data from the three highlight blocks
containing intensities for nominal masses 41, 42 and 43 amu.

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Figure 24: Example of a total counts spectrum formed from the four ASCII files shown in
Figure 23.

The conversion filter “.ion” when applied to a directory merges the data intoa single experiment frame containing one spectrum per original ASCII file, butmaintains the data for each spectrum as a single block. While the format
adopted is more traditional for mass spectra, the peak identification option
uses peak-fitting and therefore the format shown in Figure 24 is more suited
to the algorithms involved. The single block of data provided by the “.ion” isfor visual inspection of the full data set and should not be used when peakidentification is employed.

Directory Profiling
The objective addressed by the features described here, is to identify andquantify in terms of mass assignments and intensities the set of peaks
characteristic of a sample. The peak structures within a ToF spectrum areillustrated in Figure 25, where it can be seen that at least five overlapping
peaks to varying degrees are responsible for the data envelope. Peakintensity and peak position are determined for these types of peak structuresusing optimized peak modelling. The very fact that peak modelling is required
highlights the difficulty of automatically identifying all the peaks for a given
data envelope. For a directory of similar spectra, automatically identifying
mass peaks from data such as that in Figure 25 is fraught with dangers andtherefore the strategy in CasaXPS for processing directories of similar spectrais one of aiding the construction of a template spectrum, for which peakmodels are prepared to be exhaustive with respect to the data underanalysis, then the automatic application of the template models to a26

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directory of spectra forms the basis for extracting the quantitative
information for each spectrum in the directory.

Figure 25: Mass peak structure from a ToF spectrum.

The creation of peak models for each significant mass peak in a file such as
the one shown in Figure 24 is central to the profiling options in CasaXPS.
About 500 data blocks corresponding to the nominal masses potentiallyrequire the construction of regions and synthetic peaks. The success of thetemplate approach relies on the peak models adequately describing thepeaks with appropriate constraints in terms of relative positions and FWHM
to permit the peak intensities to be calculated from the fitted model. To
assist this initial step, an option on the Exact Mass Calculator property pageof the Element Library dialog window offers a means of creating peak models
based on a threshold limit.
The Create Peaks button on the Exact Mass Calculator property page (Figure26) uses the threshold value to limit the number of peaks created for a given
data block.

Figure 26: Exact Mass Calculator Property page.

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The peak creation mechanism uses the threshold value entered on the MS
Peak Threshold dialog window to create a region and synthetic peaks foreach data block overlaid in the active tile. The smaller the threshold values,
the smaller the peaks will be that are included in the peak search. Since thesignificance of mass peaks may not depend entirely on peak intensity, it isworth noting that different threshold values may be appropriate for different
ranges in the mass scale. It is therefore unlikely that a single application of
the Create Peaks button will generate all the appropriate peaks, however, by
the user selectively overlaying data blocks and choosing different thresholds,
peaks can be created on large numbers of data blocks while still retaining thediscretion of the operator. Ultimately, the success or failure of the profilingstep will depend on the way these peak models are constructed and timespent in getting these models right will be recovered by the accuracy andautomatic application of these models to larger data directories.
Profile Directory Toolbar Option
The options for profiling a directory of IonToF spectra are as follows:
1. “.amu”
2. “.fit”
3. “.vfc”
These conversion filters are used to control the nature of the directory
profile. On providing a base name followed by one of these filter strings, thedirectory located by the File Dialog window invoked by the toolbar buttonis scanned for the appropriate file types and, on accepting the Continue
prompt via the resulting message dialog, the set of files are one-by-one
processed to produce several text file reports and a VAMAS file containing
the profile information from the directory.
The two profile filters “.amu” and “.fit” both require a template spectrum tobe loaded and displayed in the active tile. In the case of the “.amu” profile
filter, the ASCII .txt IonToF files are converted to VAMAS files before applying
the template information to these newly converted data, which are also
saved in the processed state as .vms files. On completion, several text files
provide the results of the profile, one offering the context information for thenumerical tabulations located in the other files. In addition, the profile
information is presented in VAMAS format within the current CasaXPS
session.
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The second profile filter “.fit” performs the same sequence of steps as the“.amu” with the exception that the files processed from the directory are the“.vms” files. This removes the conversion step from the operation and isappropriate if, for example, the data directory has been previously processedusing the “.sum” conversion filter described above. The “.sum” conversion
filter generates a single spectrum from a set of files in a directory and also, aspart of the process, converts the ASCII files to VAMAS format. The total
counts spectrum created from the “.sum” operation may appear in the same
directory as the converted files, but provided the filename retains the “.sum”
sub-string, the total spectrum will not appear in the final profile results
generated from applying the template file to the set of .vms files in thecurrent directory.
An alternative way to profile a directory of .vms files is to apply the “.vfc”
profile filter. In this case, no fitting is performed, but rather the existing peakfits within the set of VAMAS files is used to construct the profile information.
The “.vfc” profile filter allows the individual files to be inspected and any
anomalies rectified on a file-by-file basis before creating the profile
information. It is important that the same set of VAMAS blocks and numberof synthetic peaks are used on each of the data blocks, however profiling thedirectory without automatic peak fitting allows user-intervention to override
poor fitting scenarios.

Working with ToF Spectra in CasaXPS
Time to Mass Calibration Procedures
A raw ToF spectrum is recorded in the time domain. Mass calibration of a ToF
spectrum is performed in CasaXPS by identifying a set of peaks in the datawith specific masses; then, by using these pairs of mass/time values aquadratic relationship between the time and mass scales is created. A linear
least squares procedure determines the two constants within the quadratic
expression and therefore two or more mass/time pairs must be supplied toperform the calibration procedure. The accuracy of the mass-to-time
calibration is dependent of the precision of the mass/time pairs used in theleast squares calculation; the more pairs used to compute the least squares
solution, the more tolerant the calibration will be to errors in the mass/time
specification.
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CasaXPS offers two methods for calibrating ToF MS data:
1. Peaks and corresponding masses specified using quantification regions.
2. Mouse identification of the peaks coupled with an exact masscalculator located on the Element Library dialog window.
Mass Calibration using Regions and Propagation of Regions
between Spectra
The Quantification Parameters Dialog window
provides a means ofdefining time intervals, within which systematic positions are defined(computed from a peak bounded by an interval) and linked to masses via anexact mass formula entered into the Name field for the regions.

Figure 27: Quantification Parameters Dialog Window shown three regions defined for the
purpose of calibrating the time scale to mass.

The spectrum in Figure 27 is an example of ToF SIMS data where threequantification regions are defined suitable for calibrating the time scale tomass. The mass associated with each region is entered into the Name field
and may be a numerical value exemplified by the region headed column B ora string corresponding to any exact mass formula equivalent to expressions
use on the Exact Mass property page of the Element Library dialog window.

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For example, the mass of a peak might be defined using the expression
C+H*3, which when evaluated would result in a mass of 15.0235 Daltons.
Mass Calibration
One or more time domain spectra can be prepared with calibration regions as
described above and overlaid in the active tile in the left-hand pane of theexperiment frame. On pressing thetoolbar button, each spectrum in theactive tile is calibrated using the peaks within the regions. Since multiple
spectra can be mass calibrated using a single invocation of the toolbar
button, the use of this procedure is supported by the propagation of thecalibration regions to similar spectra, thus avoiding the need to manuallycreate regions for each spectrum requiring a mass calibration.
Propagation of Calibration Regions
The procedure to propagate the calibration regions from the spectrum as
defined in Figure 27 to two other similar spectra is as follows:
1. Select the VAMAS blocks in each of the two experiment frames
containing the spectra requiring the calibration regions.

The CasaXPS window is arranged in a tiled format using the Tile option fromthe Window menu at the top of the CasaXPS main window. The arrangementof the experiment frames allows the selection to be made by left-clicking thefirst VAMAS block in the experiment frame to the bottom-left and thenholding the Control-Key down and left-clicking the VAMAS block in thebottom-right experiment frame
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2. The Browser Operations dialog window is invoked by right-clicking themouse with the cursor over the left-hand pane of the top-mostexperiment frame. The objective is to right-click over the display tile inwhich the spectrum containing the calibration regions is displayed.

3. To propagate regions to the two selected VAMAS blocks, which arelisted on the Browser Operations dialog window, tick the radio buttonin the Propagate section of the dialog window and press the OK
button. Region labels are now visible on the spectra.

The data in each of the three experiment frames are calibrated by switchingfocus between the experiment frames and each time pressing the32

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button. Control-TAB moves the focus between the experiment frames within
CasaXPS.

The time to mass calibration for the time domain data may be seen labellingthe x-axis using a quadratic mass scale.

Mass Calibration using the Exact Mass Calculator Property Page:
The procedure for calibrating a spectrum involves creating a set of
mass/time-bin pairs within the scrolled-list on the Exact Mass property pageon the Element Library dialog window.
The example below illustrates how the columns in the scrolled-list headed
Mass and Time store the information relating these two parameters. Before
an assignment for a given entry has been made, the value in the Time column
is set to -1. The mass for an entry in the table is computed from the chemical
formula entered into the name column.
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To add an entry to the calibration table:
1. Type a chemical formula into the text-field below the scrolled list andpress the Add Formula button or press the return key on the keyboard.
The formula for an ion may be entered using the chemical symbols
used to on the Periodic Table property page of the Element Librarydialog window.
2. Select the name in the scrolled-list. To select a name field, place thecursor over the text within the Name column and left-click the mouse.
The name entry will appear highlighted when successfully selected.
3. Zoom into the known peak in the spectrum displayed in the active tile.
It is important to perform the zoom operation before step 4 is taken.
4. Tick the tick-box labelled “Define Time”.
5. Using the mouse cursor, click on the known peak at a location
representative of the mass already defined by the selected entry in thescrolled list. The value in the Time column is updated and the DefineTime tick-box is cleared.
At least two entries must be specified in the scrolled-list before pressing theCalib C,t0 button on the Exact Mass property page. The more entries
assigned mass/time pairs, the better the mass to time calibration will becomputed in the least squares sense.
Once a calibration table has been prepared, a file containing the calibration
points can be saved to a separate text file from the data.
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These files can be reloaded at a later time to provide an initial calibration forother data or for making adjustments to the calibration of the original
spectrum used to create the calibration file. Note, while the Save button on
the Exact Mass property page saves the current calibration table, the Loadbutton will merge a saved file with the current set of entries on the scrolledlist. To return the table to the entries within a file, it is first necessary to press
the Delete All button. The Delete All button removes the current entries inthe scrolled-list, while the Delete Entry button removes the currently
selected entry.
If an assignment is incorrect, the individual entry must be deleted from thetable. The name field for the deleted entry is entered into the text field
below the scrolled list; therefore a selected entry can be deleted thenreinstated by immediately pressing the Add Formula button. The Time field
will return to a value of -1 and therefore be ignored during any subsequentcalibration operation.

The Element Library from a ToF Perspective
The element library in CasaXPS is an ASCII file. On startup, CasaXPS loads thedefault element library from within the same directory as the one in which
the CasaXPS.exe executable file is located. The name of the default element
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library file is CasaXPS.lib and is designed with the view that the element
library can be constructed for specific applications. For example, in the caseof quadrupole MS, a library consisting of elemental isotopes is appropriate to
the resolution of quadrupole mass spectra, while for high resolution ToF MS
a library consisting of entries for molecular fragments is required whenassigning mass peaks.
Preparing an element library file for mass spectra may be performed using a
spreadsheet program such as Excel or tools on the Exact Mass Calculator
property page allowing correctly formatted library files to be constructedfrom lists of chemical formulae. Methods for displaying the significant peaks
based on selections from an element library constructed from one or morelibrary files are described below.
The Element Library and Linking ToF Peaks for Display
High resolution ToF spectra typically consist of numerous peaks; however forsome analyses only a small number of correlated peaks are significant for
distinguishing between samples; a peak at one mass is only characteristic of aparticular compound when also accompanied by other peaks in the
spectrum. A strong link between the element library and displaying data forinspection is therefore introduced in CasaXPS 2.3.15. The objective is to use
the element library to specify a set of mass peaks grouped with respect tocorrelated peaks which are used to makes selections of VAMAS blocks. These
selections of VAMAS blocks containing narrow interval mass spectra combinewith the display tools in CasaXPS to provide a perspective in which overall
spectral distribution and localised peak structure can be assessed withrelative ease.
A ToF data set presented as a set of unit mass VAMAS blocks can be viewed
in the more traditional form of a single plot. The traditional perspective of a
ToF spectrum is achieve by selecting all the VAMAS blocks in the right-handpane, then pressing the overlay toolbar button. When viewed as a single
continuous display, all the features for manipulating the display are still open
for use.

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The advantage of creating a set of mass calibrated VAMAS files is that the
spectrum can be dissected and displayed with a variety of options:
Display only those peaks more than 5% in intensity of the largest peak.

Display one VAMAS block per tile for those peaks greater than 5% of the
maximum peak. All peaks scaled with respect to a specific peak; mass 23 inthis case.

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Scale the peaks on an individual basis.

Take a closer look at specific peaks.

Enhancements for manipulating the selection and display for ToF MS data are
available on the Element Table property page of the Element Library dialog
window.

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The mechanisms offered on the Element Table property page are describedin the following sections.
Linking Element Library Entries
A CasaXPS library file may be prepared with a set of entries corresponding toparticular sample chemistry. Such a library file can be loaded or merged withthe existing library file whenever appropriate. The essential feature of theentries in the given library file is that a set of mass formulae are all assigned
the same unique string for the Transition column.

Using the Selection Mechanism
By way of example, a set of formulae only involving carbon and hydrogen are
assigned the Transition string CH. On selecting one of the entries using theName column of the table on the Element Table property page bearing theCH Transition string before pressing the Display Linked VBs button on the
Element Table property page causes all those VAMAS blocks (in theexperiment frame with focus) to be displayed in the left-hand pane, one
VAMAS block per tile. Thus, a set of related mass peaks can be easily
displayed for inspection.

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A dialog window provides a means of only selecting those VAMAS blocks forwhich the peak intensity is greater than the specified percentage of the
maximum peak in the data.

The key used to match the VAMAS blocks in the experiment frame is thestring corresponding to the Species VAMAS field within each VAMAS block.
The Species VAMAS field is used in the header string for each column ofblocks in the right-hand pane of the experiment frame.

The ToF spectral files, when split into sets of VAMAS blocks, are created using
the appropriate nominal masses to create these Species fields and the library
entries with the common Transition library field are used to compute thecorresponding nominal mass for each library entry, which when matched to
the Species VAMAS fields causes the data to be displayed in the tile list.

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The element library file also includes Transition strings CO and F.

The different assignments for the Transition strings are simply a partition of
the file between three possible sets of mass peaks; however a more realistic
example might involve significant peaks from any combination of mass peaks,
all of which would be collectively assigned a common Transition string.
Should the same mass peak correspond to more than one compound, theelement library file can include repeated entries differing only by theTransition string.
Overlaying Related VAMAS Blocks
The Element Table property page also includes a button for overlaying
VAMAS blocks selected from the current file using the same mechanism as
the Display Linked VBs button described above.

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To overlay a set of VAMAS blocks corresponding to a predefined compound,
one of the entries in the element-table list for the compound is selected
before pressing the Overlay Linked VBs button. A dialog window appears
offering a threshold value, which represents the percentage of the maximum
height intensity of the peaks in the experiment frame. Only peaks of intensity
greater than the percentage specified on the dialog window will be includedin the set of VAMAS blocks overlaid in the active tile.
Constructing an Element Library File
The element library file was constructed using the Ex M T button on the Exact
Mass property page and three text files containing lists of chemical formulae.
An example file containing formulae used to compute exact masses forlibrary entries is as follows.

To create a corresponding library file, select the text file via the File Dialog
invoked by the Ex M T button.

The base-name for the text file is used to assign a string to the Transition fieldin the resulting library file created when the Open button is pressed on theFile Dialog window. The new library file appears in the directory where theoriginal text file is located.
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The intension is that a text file is prepared for those mass fragmentscharacteristic of a particular compound, from which a library file is thencreated. When it is desired to visually inspect a ToF spectrum for evidence ofthe given compound, the library file for the compound is loaded into CasaXPS
via the Input File property page.

The library file displayed via the Element Table scrolled list

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is a combination of loading three different library files using the Input File
property sheet. The first file was selected using the Browse button, and thenpressing the Load button caused the selected library file to replace theexisting library entries. The two remaining files were merged with the first
file by again using the Browse button to select the files followed by pressing
the Merge button.
Examining the Peak Structure using Zoom Actions
The standard method for defining a range of intensities in CasaXPS is to use
the left-mouse button to drag a box over the peaks of interest before leftclicking inside the box on the display tile. The mechanism used in thedefinition of the zoom-box is enhanced when the Element Table property
page is top-most on the Element Library dialog window. These enhancements
are enabled by holding down the Control Key or the Control Key at the sametime as the Shift Key on the key board. The result of combining the Control
Key with the Element Table top-most on the Element Library dialog window is
to create a narrow and tall zoom box at the location of the cursor whenever
the left-mouse button is clicked.

The second modification to the zoom mechanism is designed to provide ameans of creating a limited intensity applicable to the mass range currently ineffect. Holding down the Control Key at the same time as the Shift Key alters
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the behaviour of the mouse drag action such that the zoom box always
extends over the current mass range, but permits the height of the box to be
determined from the cursor’s final position.

To perform the zoom action, click inside the zoom box.
While zoom-actions permit a global perspective of a spectrum to betransformed into the display of a specific peak, there is always a costassociated with mouse actions required when transforming the display to see
the peaks located at a nominal mass. The problem lies in the sparse nature of
the mass peaks compared to the number of data bins comprising a spectrum.
It is for this reason that the nominal masses can be broken down into
individual VAMAS blocks using the Display Linked VBs button on the Element
Table property page described above, thus offering a means of individuallydisplaying a user defined set of VAMAS blocks. When these blocks are
displayed, each spectrum appears such that the intensity scale is appropriate
for each and every VAMAS block. However, while ensuring the peakstructures are visible, the relative scale of these data, when viewed as
individually scaled tiles, is lost. For this reason new SIMS toolbar buttons
are introduced to permit the intensity scale for the entire set of data
displayed in the left-hand pane of an experiment frame to be determinedfrom the active tile. These toolbar buttons when coupled with the extension
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within each VAMAS block to be visualized with a similar perspective ofintensity as that seen in an overlaid plot of the data. The following display
shows two rows of VAMAS blocks after scaling with respect to the tile withheading 43.

The Page Tile Format dialog window provides the means of adjusting thenumber of tiles per row and the Tile Display Parameter dialog window offers
display settings for switching the tile display to those seen. The organizationof the VAMAS blocks in the scrolled list means that paging down the scroll list
effectively scrolls through the mass range in the spectrum being displayed.
The enhanced Page Tile Format window
provides the means of changing
the number of tiles per scroll position in the left-hand pane of theexperiment frame.

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To display the VAMAS blocks without an x-axis, the Tile Display Parameters
dialog window is used.

Profiling Features for ToF data

Figure 28 ToF Mass Spectrum displayed using Time Bins. Data provided by Prof. Winograd,Pennsylvania State University, USA.

ToF MS is often categorized according to the method for generating the ionsfrom the sample. The data in Figure 28 is an example of Secondary Ion Mass
Spectrometry SIMS, where the ToF technique is used to separate ions withdifferent mass-to-charge ratio following exposing the sample to a focused
beam of ions from an ion gun. Since the beam from the ion-gun can bescanned across the sample surface, ToF data may be collected over a set ofpoints on the sample. Knowledge of where on the sample a time event wasrecorded allows the spectral data in Figure 28 to be assigned to pixels in mass
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to the peaks identified in Figure 28, that is, each image is obtained by only
counting time-events contributing to the peaks labelled on the spectrum.

Figure 29: Mass resolved images extracted from the ToF SIMS data file corresponding to thehistogram Figure 28.

Similarly, identifying pixels in an image and only counting time-events
corresponding to the selected pixels permits multiple spectra to be extracted
from a single ToF data file. Given the complex nature of ToF spectra, theability to retrospectively examine the data from an experiment is a powerfultool in understanding the information in the spectra.
ToF MS is used to obtain spectra through ionization mechanisms other than
SIMS. Proton Transfer Reactor (PTR) ToF MS (Figure 30) provides a soft
ionization mechanism of an analyte by the transfer of a proton from H3O+ tothe analyte. While spatial information is not appropriate for PTR ToF MS, thetechnique provides temporally separation of spectra, where variation ofmass-peaks with time provides a profile (Figure 31) of changes in a sample.

Figure 30: Schematic of a PTR ToF MS (Kore Technology Limited, UK)48

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The tools for the purpose of visualizing the data from a ToF MS experimentare described in following sections.

ToF Data File Options
The options on the SIMS toolbar for manipulating ToF MS data fall into two
categories: those for which a new VAMAS file is created without reference toother data and those for which an existing spectrum or image is used tocreate spectra or images representing a subset of the data within a file.

Figure 31: A profile of PTR ToF MS peaks.

Currently, two types of file formats may be processed using these options:
Kore Technology Limited list files and Prof Winograd’s (Pennsylvania State
University) Bio ToF XYT files. Both types of files contain time information as
well as associating the time information with image pixels.
The first step to viewing a data file is to create a spectrum from the entire fileof time values regardless of whether the file is a set of images or a profile ofsome description. From the total spectrum, peaks are identified from which
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images or profiles are created. In turn, the images or profiles can be used todefine the pixels or layers of interest, which once specified are used to extra
pixel or layer filtered spectra from the original data file.
Create a Total Ion Spectrum
A total ion spectrum is created from a data file specified using the resulting
File Dialog window shown in Figure 32.

Figure 32: Convert to VAMAS File Dialog window used to specify the ToF MS files.

The file types supported are:1) Files with the extension “lst” created using by the Kore Technology Ltd ToF
MS instruments. The lst files contain a list of binary data in which eachanalysis ToF cycle appears as a sequence of start events followed by a list of
stop events representing ions arriving at the detector. While these analysis
cycles may be associated with a pixel in an image or a layer of a profile, thespectrum created from the lst file ignores these distinctions and generates asingle time histogram from the timing information. Images or profiles aresubsequently generating from the list file using the total spectrum as areference.
2) Files with the extension “xyt” created from the Penn State University Bio
ToF instrument. The xyt files are binary files containing a two dimensional
array of lists, where each pixel in an image is associated with a list of stop
events specifying the arrival times of ions at the detector. The total ion
spectrum is created by ignoring the spatial information and generating ahistogram from the entire set of time lists.
3) Files with the extension “spc” generated from the Kore Technology Ltd
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histogram. No image or profile information is present in these files. Sets of
spc files within a directory can be profiles using the options below.
4) Files with the extension “dat” generated from the Penn State University
Bio ToF instrument. The dat files are already in the format of a time binned
histogram. No image or profile information is present in these files. Sets ofdat files within a directory can be profiles using the options below.
Creating a time spectrum from a raw data file
involves selecting the filewith the appropriate file extension using the File Dialog window shown in
Figure 32. Once a file is converted and displayed in an experiment frame, thedata can be selectively processed using information defined on the total ion
spectrum.

Figure 33: Total Ion Spectrum from an Image File.

The spectrum in Figure 33 is a total ion histogram which is mass calibrated
and prepared with quantification regions in anticipation of processing a set ofimages from the raw list file. The quantification regions define the timeintervals over which ions are allocated to pixels in images as the list file isprocessed a second time. Figure 34 represents the outcome to the second
pass through the list file; the images are obtained from the second pass by
only collecting and allocating counts to images in accordance with thequantification regions define on the spectrum in Figure 33.
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Figure 34: Images processed from the list file corresponding to Figure 33.

The steps taken to create these images will now be described.
Create Images from Spectra using Quantification Regions
Once a total ion spectrum is available, the data can be mass calibrated using
one of two procedures: 1) define a set of calibration points in the form of(time, mass) pairs via the Exact Mass Calculator on the Element Library dialog
window or 2) define a set of calibration regions using the Quantification
Parameters dialog window and calibrate the spectrum using a button fromthe SIMS toolbar. While it is not necessary to calibrate the time bin spectrum
before generating images, given a time-to-mass calibration the automatic
region creation option on the Element Library dialog window will assign thenominal mass to the region names and therefore aids the interpretation of
the data.
Defining Quantification Regions using the Find Peak buttons
Regions defined on the total ion spectrum provide the time intervals overwhich counts are accumulated into images. The Quantification parameters
dialog window permits regions to be created one at a time, however ToF MS
is typically blessed with numerous peaks and creating a region for each ofthese peaks manually would be too time-consuming. As a result, the Element
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Table and Periodic Table property pages offer Find Peak buttons, which for
ToF data will create a region for each peak subject to a threshold criterion.
While the regions are created by simply pressing the Find Peaks button on
the Element Table property page, it is worth reviewing the limits of theregions using the Resetand Zoom Out
toolbar buttons. When the
Reset button is pressed, any regions created on a spectrum are loaded onto
the zoom-list. Thus pressing Reset followed by repeatedly pressing the Zoom
Out button will step through the regions created by the Find Peaks button.
The limits for the regions can be adjusted under mouse control provided theRegion property page is visible on the Quantification Parameters dialog
window.

Creating the Images
The total ion spectrum retains a record on the file from which it originated,
therefore pressing the toolbar button
with toolbar hint List File to Images
will cause the original list-file to be scanned a further time. During the second
scan of the list file, counts are accumulated into images defined by thecurrent set of regions on the spectrum displayed in the active tile. Note,regions created automatically may be numerous and therefore the resulting
image data file is potentially large. The operation is similarly potentially time
consuming and may take several tens of seconds, depending on: the number
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Copyright © 2010 Casa Software Ltdof regions as well as the processor power, memory and disk speed of the PC
performing the operation.
The spectrum in Figure 33 was used to create the images displayed in Figure
34 via thetoolbar button.

Spectra Generated from Image Zones
Given an image of the sample, a false colour scale defined over intensity
ranges offer a means of specifying which pixels from the image should be
included in the procedure for creating time-bin histograms from the list file.
As a result, one or more spectra can be extracted from the list file which will
be referred to as LUT spectra (Look-Up Table); the colour used to display apixel in a false colour image is defined using a “look-up table” of colour
values.
The image in Figure 35 is an example of a mass resolved image displayedusing a false-colour-scale consisting of four colours. The intensity scale ispartitioned into the false colours defined using intensity ranges characteristicof the implanted gallium lettering PSU and the complementary pixels to thegallium lettering. Four spectra are generated from the list file based on thefour false colours defined on the image by only collecting time events
corresponding to the pixels displayed using the false colours. A comparison ofthese LUT spectra for the gallium mass range is made in Figure 36.

Figure 35

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1. Select an image generated from the original total ion spectrum for alist file.
2. On the Image Processing dialog window, available from the Options
menu, select the Colour Scales property page.

Figure 36

3. Select the False radio button from the Scale Type list and press the
Apply button.

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4. Mark a range on the image colour scale displayed next to the image inthe left-hand-side of the experiment frame using the cursor whilst
holding down the left-mouse-button.
5. Press the button labelled Add False Colour. The colours, as specified by
the dialog window which appears when the button is pressed, aredisplayed in the colour scale in the active tile and the image itself is
updated using the newly define false colour.
The default false colours are ordered to agree with the colours used todisplay spectra when overlaid in a tile.
6. Once the desired zones of pixels are assigned false colours, the image
can be made the current template using the Define Image on the
Image Processing property page.

7. To generate the LUT spectra press thetoolbar button. The list filecorresponding to the image is scanned and, for each false colour in theimage defined by the previous step, a spectrum is added to a newexperiment frame.
Creating a Profile from a Total Ion Spectrum
The concept of a ToF list-file is applicable to time dependent measurements
where spectra evolve during the course of an experiment. The data fromsuch an experiment can be treated as a total ion spectrum. Just as the datafrom an image can be interpreted as a large area analysis to produce a single
spectrum from all the data, so too can all the ToF timing information beinterpreted as a single spectrum; the difference being that, in creating thetotal ion spectrum the for a profile, all the changes over time are ignored.
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Figure 37: PTR ToF MS total ion data showing quantification regions prepared for the
purpose of creating time-dependent intensity profiles.

The total ion spectrum in Figure37 provides a coarse description of theexperiment, from which the time dependent information can be extracted.
The procedure used to plot the variation of the spectra with time is similar tothat of extracting images from an image list file, that is, quantification regions
are assigned to the mass-peaks on the total ion spectrum followed bypressing thetoolbar button. The total ion spectrum maintains a reference
to the original list-file, therefore on pressing the toolbar button, the list-file isscanned a second time producing a trace for each quantification region
defined on the total ion spectrum.

Figure 38: A plot of three traces from the regions defined on the total ion spectrum in Figure
37.

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The data in Figure 38 represents three quantification regions from theregions defined on the total ion spectrum in Figure 37. The oscillations in the
profiles are due to changes in the air sampled from a subject whilst themastication of food is performed.
Spectra Generated from Profile Layers

Figure 39: Spectra generated from the regions defined on the profile in Figure 38.

Given a profile such as the one on Figure 38, spectra corresponding to arange of times or cycles can be generated as illustrated in Figure 39. For eachquantification region defined on a profile, (Figure 38 includes two suchregions) a spectrum is obtained by summing only those times falling into theranges specified by the regions.
Quantification regions are added to a profile using the Quantification
Parameter dialog window. Given the two regions in Figure 38, pressing thetoolbar button causes the list-file to be read a further time accumulating
the spectra from the timing data. The spectra in Figure 39 are examples ofdata collected from layers within a profile experiment.
Create a Profile from a Directory of Files
So far, ToF list files have been considered as the data structure managing
images of spectra or profiles of spectra. The extension to the concept of a list
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file is a directory of list files, where each list file represents a change in termsof the experiment performed. For example a depth profile of image list files
offers the possibility of measuring an image of spectra for each layer within asputter depth profile. The experimental conditions evolving during the courseof the experiment are the depth beneath the surface at which an image ofspectra is acquired. Such experiments are by nature time consuming andlarge in data size.
Creating a profile from a directory of list files involves selecting a
representative spectrum from the directory of list files suitable for specifying
the mass calibration and also the set of peaks to be profiled throughout thedirectory of files.
The active tile must display a spectrum for which regions are defined suitable
for mass calibration. Once the spectrum is prepared the process is initiated
via thetoolbar button. A File Dialog window allows the specification of adata directory containing the files for which the list files are processed asfollows:
1. Converted to spectrum VAMAS files.
2. Each spectrum is mass calibrated using the regions defined on the
spectrum in the active tile.
3. Peaks identified using an automatic threshold search and regions
created for each of these peaks identified.
4. The region intensities are collected into profile traces for each region
created in the peak identification step.
5. A new experiment frame created using the name specified on the Filedialog window.
Initially the directory of list files appears as follows.

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Each file with the directory is processed during the course of the profile
procedure. On completion, the same directory appears with a VAMAS filecorresponding to each original list file plus one further VAMAS file containing
the profile traces for each peak identified as significant. After processing thedirectory appears as follows.

Before pressing the Profile from Files
toolbar button, a spectrum must be
displayed in the active tile prepared with regions sufficient to provide anadequate mass calibration.

The file name for the profile with the appropriate list-file extension, enteredin the Filename text-field on the File dialog window, specifies the type of list
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operation is initiated. These files tend to be large; therefore the time taken tocomplete the profiling task may be large too.
When the profile is complete, a new experiment frame opens in CasaXPS andthe profile traces are displayed. A typical profile file will contain numerous
profile traces.

Convert and Merge a Directory of XYT FileAn alternative to automatic profiling a directory of list files is to analyses thedepth profile using the set of total-ion spectra converted from each XYT filein a directory.

A profile experiment, in which a sequence of images is acquired into separate
XYT files, can be investigated in terms of the total ion spectra using thetoolbar button. A File Dialog window is used to specify both the directory
containing the XYT files and the name of the file created by scanning thedirectory for XYT files; the XYT files are individually converting into VAMAS
files containing the total ion spectra. After each XYT file in the directory isconverted, the set of VAMAS files are merged into a new experiment frame.

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Figure 40: Merged XYT files

To load a directory of XYT files into a new experiment frame, select the
toolbar button to invoke a File Dialog window; move to the directory
containing the XYT files then enter a name into the file name text-field withthe file extension “.xyt”. ToF spectra tend to require large quantities ofmemory, therefore take care not to attempt to merge an excessive numberof file as the operation may take considerable time to complete.
Once a set of spectra are loaded into an experiment frame, trends within thedata can be assessed using the Custom Report mechanism on the Report
Spec property page of the Quantification Parameters dialog window shown in
Figure 40. A set of profiles determined from the data in Figure 40 are
displayed in Figure 41. These profiles are obtained by defining a set ofquantification regions using the Regions property page, generating an Area
Report using the Custom Report on the Report Spec property page thencreating a new VAMAS file from the tabulated report via the Create Profile
menu option on the File menu.

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Figure 41: Profiles generated from the merged spectra shown in Figure 40.

Image Depth Profile Data Analysis
Given a directory of xyt files:
Create an experiment frame containing a profile set of images
corresponding to the set of regions defined on a spectrum in the active tile.

Figure 42: Set of images created by accumulating counts into pixels based on regions definedon a spectrum.

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Figure 43: Spectrum used to create images in Figure 42.

The images displayed in Figure 42 were generated from a directory of XYT
files, where data from the XYT files are processed only for those counts fallingwithin the time windows specified by regions defined on the associatedspectrum in Figure 43.
Three regions were defined using a total ion spectrum. The spectrum must be
displayed in the active tile before pressing thetoolbar button. The
operation involves reading the entire set of XYT files in the directory specified
via the File Dialog window. The process is potentially time consuming. To
process a directory of XYT files, a file name must be specified in the File nametext-field on the File Dialog with extension .xyt. On completion, a new VAMAS
file is created with the name specified concatenated with the .vms fileextension.

Figure 44: False colour image used to generate profiles in Figure 45.

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The Image Processing dialog window on the Options menu offers tools forprocessing these sets of images. For example, the false colour image scale
defined on the image displayed in Figure 44 may be used to generate depth
profiles for the sum of pixel based on coloured zones.

Figure 45: Profiles constructed from a directory of XYT files using the false colour image in
Figrue 44.

Creating the profiles in Figure 45 requires the generation of LUT spectra fromthe directory of XYT files. Regions defined on the LUT spectra coupled with
the Custom Report on the Report Spec property page of the Quantification
Parameters dialog window provide to tools to create the profiles based on
false colours.

Figure 46: Spectra collected using the false colour image in Figure 44.

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Generating LUT Spectra from a Directory of List Files
Spectra from False Colour Zones
Given a directory of XYT files and a false colour image, thetoolbar button
creates a new experiment frame containing a set of spectra from each XYT
file, where the spectra are accumulated from the time information from only
those pixels identified by the false colours in the image. For example, thefalse colour image in Figure 44 is the sum of all the gallium 69 isotope images
and therefore the colour zones are determined by the gallium distributed
throughout the volume sampled by the depth profile. Spectra from thesefour colour zones are collected into the new experiment frame shown in
Figure 46, thus the depth profile can be examined from the perspective ofgallium using these spectra.

Quantification Reports and ToF Data
The intensity associated with a ToF mass spectrum represent ions counted at
a detector. The time element of the measurement is less important than isthe case for other techniques where a specific data channel is monitored fora specified time; data under these measurement conditions are typicallyquantified in terms of counts per second (CPS). For ToF Data, the pulsed
extraction of ions and the delay required to allow ions to traverse the flighttube result in a departure from the need to consider counts per second, butrather to focus on the number of ions detected. CasaXPS generally assumes
data are quantified in terms of CPS and peak areas are integrated withrespect to the independent variable. Since the default quantification regime
in CasaXPS is not appropriate for ToF data, there are ToF motivatedconfiguration options to permit quantification of ToF intensities in terms of asummation of counts over time or mass bins.

Quantification via the Report Spec Property Page
The Report Spec property page of the Quantification Parameters dialog
window offers two methods for generating quantification reports. The
Standard Report is predominantly aimed at tabulating results on a spectrumby-spectrum basis; while the Custom Report is designed to support the
profiling of data acquired sequentially, for example a depth profile.

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Standard Report
The Standard Report permits quantification in terms of quantification regions
and/or synthetic components. For ToF data, quantification based on numberof ions requires the specification of appropriate configuration files. These
configuration files are located in the directory called CasaXPS.DEF.

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Generating a quantification report for ToF data requires the use of ASCII
configuration files named:
Report Button Pressed
Quantification Regions
Synthetic Line shapes
Regions and Comps

Configuration File Name
RegionQuantTable.txt
ComponentQuantTable.txt
RegionComponentQuantTable.txt

The configuration files can be edited using Notepad or any other text based
editor.

The format for the files is a list of keywords entered one per line, where eachkeyword specifies the type of information appearing in each column of thetext quantification report generated when the corresponding button on theStandard Report is pressed.

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A quantification report is created for those VAMAS blocks selected on theright-hand pane of the experiment frame with focus.

On pressing the Regions button from the Standard Report section with the
Use Config File tick-box tricked, the following report is produced:

For ToF data, the important column is the one specified using the keyword
SIMS_PEAK_AREA in the RegionQuantTable.txt configuration file. The
columns in the quantification report have a one-to-one correspondence withthe keywords entered in order one-per-line within the RegionQuantTable.txt
file.
The quantification report is exported as a tab spaced ASCII data set throughthe clipboard. To move the quantification report to a spreadsheet, forexample, press the Copy button on the top toolbar. A clipboard dialog
window offers the option to save the data to file or copy the data onto the
clipboard.

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The data on the clipboard can be pasted into another program such as Excel.

Custom Report
The profiles in Figure 45 were created using quantification regions and theCustom Report section on the Report Spec property page.

Since ToF intensities are determined from the number of ions within a peakand not the peak area, quantification items defined on the spectra, either
regions or components, must include a keyword in the Tag field and thereport must be generated using the Tag Defined Report button. To indicatethat a region or component derives from ToFSIMS data, the keyword tofsims
must be entered in the Tag field for the quantification item.
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The Tag Defined Report button uses the keyword in the Tag field todetermine the type of data to retrieve from the quantification item. The
keyword tofsims causes the summation of the counts within the region orunder the components on a bin-by-bin basis. Other keywords include height,
which returns the maximum peak height as the measure for intensity. Note:for both keywords tofsims and height, the intensities are divided by the value
entered in the RSF field; therefore the number of ions recorded for a given
peak is only obtained for an RSF of unity.
A further word of warning: the Custom Report is defined in terms of a list ofnames and formulae. The formulae are constructed from the name fields
used to specify the quantification items. There is no difference between how
regions and components are treated within these formulae, both areconsidered to be quantification items and intensities from regions and/or
components can be combined to create a quantification report. A key
property of the Custom Report is that, intensities from either regions orcomponents or both with the same name field are automatically summed
together. To be sure that the profile is from exactly the intended items,
always use different names for items included in the profile.
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An Overview of Working with ToF Data in CasaXPS
The SIMS toolbar is displayed via the View menu on CasaXPS.

The SIMS toolbar offers a range of options for displaying and manipulating
ToF MS data.
Display Options:
ToF Time to Mass Calibration Options:
Organization of Data:
Data Conversion Options:

SIMS Toolbar Buttons: Display Options
The toolbar button switches the display setting between forcing data to
be displayed with a lower intensity of zero and allowing a selectable lower
limit. The default state for the display of ToF MS spectra is to force a lower
limit of zero. A line is drawn at the bottom of the tile to indicate when thedisplay is forced to plot intensities above zero intensity. When the line
appears at the bottom of the tile displaying the ToF spectrum, a zoom box
drawn over the display will only indicate the upper limit for the purposes of
expanding the display.
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On left-clicking inside the zoom box with the zero base line active the display
becomes:

Toggles the display between log and linear display modes:

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Overlay selected VAMAS blocks by column:

Given a selection of VAMAS blocks in the right-hand pane, display eachcolumn of VAMAS blocks in separate tiles in the left-hand pane. Each tile isscaled with respect to the spectra displayed within the tile.
Adjust the scale for the tiles displayed in the left-hand pane withrespect to the intensity range determined from the active tile.

Adjust the scale for the tiles displayed in the left-hand pane withrespect to the intensity range currently used in the active tile and toggle themode for the y-axis display.

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Display state modified by the toolbar button are as follows:
Off

On

Cycle the display through a set of predefined mass ranges.

A spectrum displayed in the active tile changes the mass range used to viewthe data each time thetoolbar button is pressed. The mass range isalways anchored by the smaller mass limit and with each press of the button
the size of the display range cycles between 5 amu, 10 amu, 25 amu, 50 amu
and 100 amu.
Step the mass range towards higher mass values or towards lower
mass values. The current mass range determines the size of the step. On
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pressing either toolbar button, the mass range is stepped by half the interval
currently being displayed.

Expand the display range about the central mass defined forthe active tile. The SIMS toolbar button increases the mass range about thecentral mass for each press of the button without rescaling the intensity
range. The equivalent button on the second toolbar performs the same
operation as the SIMS toolbar button with the exception that the button on
the second toolbar also rescales the intensity range.

Step the current mass range by one amu. The intensity scale isunaltered by pressing either of these buttons.
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Given a spectrum displayed in the active tile, the toolbar button adds a
set of tiles to the scrolled list of tiles in the left-hand pane, where the display
range in the active tile is split into sub-ranges, the number of which is defineon the dialog window invoked by the toolbar button. The display before
pressing the toolbar button:

Result of splitting the full spectrum into eight sub-ranges, one per tile isshown below:

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Each sub-range is rescaled within the display tile. Note that if the number oftiles exceeds the number of tiles-per-page in the left-hand pane, theadditional tiles cause the scroll-list to expand indicating the existence offurther pages of display tiles.

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SNMS in CasaXPS
An Overview
Sputtered Neutrals Mass Spectrometry (SNMS), as a technique related to
SIMS, is supported on the Dynamic SIMS dialog window of CasaXPS.
The Dynamic SIMS property page is available from the SIMS toolbar
The SIMS toolbar is displayed using the View menu on the CasaXPS Main
Window menu bar.

Quantification of SNMS profiles requires the calculation of sensitivity factors.
These SFs are calculated using options on the SNMS RSF Calculator property
page.

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Relative SFs are SFs normalised with respect to a given isotope. Both SFs and
RSFs are determined based on measurements from standard materials. Onceestablished for a set of isotopes, data measured under identical conditions
can be quantified in terms of either Atomic concentration or Massconcentration using options on the SNMS RSF Calculator property page.
Further tools for transferring RSFs to other measurements are available on
the Prepare Profile property page.

The function of the Prepare Profile property page is to copy RSF and sputterrates to multiple data files with the view to generating quantified profiles
from the raw SNMS data. The buttons on the Prepare Profile property pageare designed to work based on selections made within the set of opened
files. To this end, other buttons on the Prepare Profile property page provide
a means to make selections appropriate for the action buttons.
SNMS and Dynamic SIMS are specified in CasaXPS using an identicalframework. The RSF and sputter-rates are assigned on a measurement-cycle
by measurement-cycle basis. In both SNMS and Dynamic SIMS, a profile fully
prepared for quantification must have each cycle populated with RSF andsputter-rates as viewed via the Calibration property page of the Dynamic
SIMS dialog window.
The sputter-rate for a given profile is calculated using the Calibration
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sputter-rate and appropriate RSF entries are updated. The table on the
Calibration property page displays the parameters used during quantification.

Basics of CasaXPS
Converting Data
CasaXPS native file format is ISO 14976 VAMAS file. CasaXPS contains many
conversion filters available from the Convert menu option on the File menu
or via the top toolbar.

Converting data involves selecting the data file with the appropriate fileextension via the Convert to VAMAS file dialog window.

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For example, Hiden data is saved in comma separated format with fileextension csv. On selecting a file containing Hiden data format with theextension csv, CasaXPS will convert the data to VAMAS format and write a
new file into the same directory as the original csv file.

The VAMAS file will then open as an Experiment Frame in CasaXPS.

Data Viewed Via an Experiment Frame
A profile experiment contains one or more traces measured and recorded foreach isotope monitored. The Experiment Frame in CasaXPS displays the datausing two panes with an adjustable central divider.
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The left-hand-pane displays the data in graphical form.

The right-hand pane offers the data blocks within the VAMAS file.

The right-hand pane is used to make selections from the set of VAMAS blocks
held within the VAMAS file. These selections are used to display subsets ofdata within the file and direct processing operations to specific data blocks.
Displaying Data
Individual VAMAS blocks appearing in the right-hand pane are displayed bydouble-clicking the left-hand-mouse button with the cursor over the data
block.

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Selecting more than one VAMAS block in the right-hand pane and using theOverlay toolbar button causes the selected VAMAS blocks to be displayed in
the active display tile.

Selecting VAMAS Blocks
Selections are made using the right-hand pane:
1. Single click the left mouse button over the right-hand pane to select asingle block of data.
2. Hold the Shift-Key down and single click the left mouse button over adifferent block in the right-hand pane to make a range selection.
3. To add to or remove from the current set of selected VAMAS blocks,
hold the Control-Key down before left clicking the mouse with the
cursor over a VAMAS block in the right-hand pane.
4. Use the Select menu to extend a selection to other VAMAS blocks ofsimilar identity in other files.

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Tile Display Options
The left-hand pane of an Experiment Frame displays the data in the form of
profiles, spectra or images. Options affecting the display are managed using
the Tile Display Parameters dialog window. The Tile Display Parameters
dialog window is invoked via the top toolbar
Options menu

or from theWhen plotting a profile involving multiple traces, a common requirement isto place a Legend or Key within the tile in which the data are plotted. The
Display property page on the Tile Parameter dialog window provides control
over placing a Key on either the right-hand side of the graph area oralternatively the left side via the Draw Key and Key on Left tick-boxes.

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The Display property page also allows the profiles to be plotted using lines,
points or both lines and points.
Display Colours
The colours used to plot the profiles are specifies using the Colours property
page on the Tile Display Parameters dialog window.

To modify the colours used to display the profiles, press the button on the
Colours property page on the Tile Display Parameters dialog window labelled
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before pressing the OK button on the Colour dialog window followed by
Apply or OK on the Tile Display Parameters dialog.

The order for the colours used to display the profiles is determined by the
Custom Colours moving left to right then top to bottom as view on the
Colours dialog window. Further, the order of the VAMAS blocks displayed in
the Active Tile is determined by the order in which the data blocks are
selected in the right-hand pane.

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Holding the Control Key down allows the order of the data blocks to change
and therefore the colours change accordingly.

Calculating SNMS Sensitivity Factors
The task of calculating a set of sensitivity factors for SNMS requires astandard sample of known composition and a measurement from thestandard sample, where a specific set of isotopes for which sensitivity factors
are to be determined is used to monitor the sample-composition in terms ofcounts per second. The SNMS RSF Calculator determines a set of factors
relating the amount of substance to the signal measured. Thus thesesensitivity factors provide the scaling factors to convert measured signal toamount of substance for profiles measured from samples of unknown
material composition. The calculation of SNMS sensitivity factors is
performed using the SNMS RSF Calculator property page on the Dynamic
SIMS dialog window.

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An example of a standard sample is a Hastelloy material for which thecomposition is known to be:
Element
Cu
Ni
Cr
V
Mo
Co
W
Fe

% Composition by
Weight
0.2
51.5
16.15
0.22
17.1
1.5
4.29
7.3

When measured using a quadrupole mass spectrometer, the recorded signal
from the Hastelloy sample defines the instrumental response for the given
sample composition.

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Armed with the experimental data measured from the standard and the tableof material compositions, the sensitivity factors for the isotopes used in theexperiment are calculated by populating the table on the SNMS RSF
Calculator property page and defining a quantification region for each
VAMAS block. The quantification region provides a means of estimating
representative signal intensity for each profile.

The information used to calculate the sensitivity factors is recorded in the
VAMAS blocks for each of the profiles. It is therefore necessary to update theappropriate information for each of the VAMAS blocks representing the datameasured from the standard sample.

To update the information needed to compute the sensitivity factors, repeat
the following steps for each isotope in the SNMS profile measured from thestandard sample.
1. Double-click a VAMAS block in the right-hand pane.

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2. Select the type of percentage known about the composition of thesample and enter the value for the percentage in the text-field.

The Update Value button becomes active as soon as a value is entered for thepercentage composition.
3. Check that the correct mass per mole and isotopic mass are displayed
and press the Update Value button.
The table on the property page displays the values currently available for
profiles displayed in the active tile.

The mass per mole is determined from the average mass for a given element,
while the isotopic mass represents the mass of the peak used to measure theprofile signal.
The table is only updated when the Update Values button is pressed.

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Each VAMAS block holding the data from a profile must be updated with thecomposition information. Overlaying the VAMAS blocks for the full profile in
the active tile causes the table on the SNMS RSF Calculator to display the fulllist of quantification information.

The table reflects the percentage composition for the standard sample. To
relate these percentage compositions to the signal intensities for the set ofprofiles, it is necessary to specify a representative intensity for each isotope.
The representative intensity is determined as the average over a set ofacquisition cycles as specified via a quantification region. Specifically, thesignal intensity is the average intensity over the set of data cycles defined by
the first quantification region for each VAMAS block in the experiment.
4. Create a quantification region for each VAMAS block, where the limits
to the region define a set of data channels over which the intensity can
be averaged and assumed to be representative of the signal measured
for the isotope being profiled.
The quickest means of creating quantification regions on SNMS/SIMS data is
to use the Calibration property page on the Dynamic SIMS dialog window.

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Overlay all the VAMAS blocks in the active tile before pressing the Define
Surf/BG button on the Calibration property page.

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The Define Surf/BG button creates two quantification regions per VAMAS
block overlaid in the active tile. Only the first region, assigned the name Peak,is used to determine the signal intensity for the SNMS data. The reason two
regions are created is to allow dynamic SIMS experiments to define a surface
zone and a zone representative of the background signal to a SIMS profile.
The quantification regions are so named because of their use in XPS data
analysis. For the purposes of SIMS and SNMS, the regions only defineintervals. Should these intervals need changing from the default values
obtained by pressing the Define Surf/BG button, the Regions property pageon the Quantification Parameters dialog window provides a means of making
changes to these interval limits.

Each VAMAS block must be updated with any changes to the region limits.
Quantification regions are propagated from one VAMAS block to others byselecting the range of VAMAS blocks in the right-hand pane of theexperiment frame and right-clicking the mouse over the left-hand pane
displaying the data with the modified regions. A dialog window appears
offering the ability to propagate the regions to other VAMAS blocks listed on
the dialog.

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Tick the tick-box in the propagate section and press the OK button. A further
dialog window appears requesting confirmation, which should be acceptedby pressing the Yes button.

Assuming that the background region is deleted and the Peak region adjusted
to provide a representative average signal from each profile, the appearanceof the set of profiles changes as follows.

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Following the creation of an appropriate quantification region, the SNMS RSF
Calculator property page will show the average value determined from theregion for the first VAMAS block displayed in the active tile.

The VAMAS file for the standard sample is now ready to calculate thesensitivity factors for the measured isotopes.
VAMAS blocks used in the calculation of the sensitivity factors must be:
1. All overlaid in the active tile
2. The table on the SNMS RSF Calculator property page displays thecorrect percentage compositions , Mass per Mole and signal isotopic
mass
3. A region is defined on each VAMAS block.
Once the data are prepared appropriately, pressing the Calculate SF button
calculates and adds sensitivity factors to the table on the property page.

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Alternatively, relative sensitivity factors are calculated by first selecting anentry in the Name column of the table before pressing the Calculate RSFs
button.

A dialog window report the reference isotope by name and on pressing OK,
the table is populated with RSF with respect to the indicated VAMAS block.

In both cases, the RSF or SF values are also entered into the VAMAS blocks ona cycle-by-cycle basis, which can be verified via the Calibration property pageof the Dynamic SIMS dialog window.

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Quantification of SNMS Profiles
Isotopic profiles are quantified by applying the sensitivity factors to theintensities measured from the sample. These sensitivity factors aremaintained within profiles measured from standard materials of known
composition. The quantification of a profile is therefore achieved bytransferring the appropriate sensitivity factors from these standard materials
to the unknown material, establishing the sputter-rate for the material underanalysis, followed by calculation of the percentage atomic or massconcentrations. The result is a new experiment frame containing thequantified profile. The process will be illustrated by quantifying a stainlesssteel sample using sensitivity factors determined from a Hastelloy material of
known composition.
Quantification of Stainless Steel using SNMS: an Example

On conversion, the data from a stainless steel sample appears in CasaXPS,
viewed via the Calibration property page of the Dynamic SIMS dialog window,
as a set of VAMAS blocks in the right-hand pane of an experiment frame.

The Calibration property page shows that initially the profiles are all assigned
an RSF of unity and a unit sputter-rate.
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RSFs and sputter-rates are defined on a cycle-by-cycle basis. This allows
values to be adjusted depending on the point in a profile at which theintensities are measured. In multilayer materials permitting differing RSFs
and sputter-rates may be important; however for a uniform stainless steel
sample all cycles will be assigned the same RSFs and sputter-rates
independent of depth.
The Prepare Profile property page on the Dynamic SIMS dialog window
provides the tools for transferring RSFs and sputter-rates between profiles.

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To transfer the RSFs from the Hastelloy standard to calibrate a stainless steel
sample:1. Load both the Hastelloy profile (previously processed to include thesensitivity factors) and the stainless steel profile.
Data converted from Hiden files include VAMAS fields defining the element
and species for the VAMAS blocks. While these strings are only important inas much as profiles from the same isotopic peaks must be assigned identicalstrings, the actual strings are at the users discretion. The Hiden data labels
the mass peaks with the nominal mass such as “Mass 58”. These element andtransition strings are used to make global selections within the set of open
VAMAS files; also the transfer of RSF and sputter-rate values is achieved via
the Prepare Profile property page based on these strings. Therefore, aconsistent assignment for these fields significantly aids the speed of datapreparation leading to quantified profiles.
2. Tile the experiment frames within CasaXPS so that the right-handpanes can easily be seenIn this example only two files are in use so tiling the opened files using theWindow menu is relatively easy. When more files are involved, a cascade ofexperiment frames can be more useful a means of monitoring the selections
within the file set.
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3. Select the VAMAS blocks within the Hastelloy standard previously
prepared with appropriate sensitivity factors.
4. Press the
button to match the selection from the
Hastelloy experiment frame throughout the opened VAMAS files.

5. Ensure that the source experiment frame is the experiment frame withfocus.

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6. Press the

button.

A dialog appears listing the set of VAMAS blocks together with the file names
from which the VAMAS blocks belong.

7. To transfer the RSF from the source file to the destination VAMAS
blocks, press the OK button on the dialog.
The key point to note is that the RSFs are copied only to those VAMAS blocks
for which the source VAMAS block element/species strings match the target
element/species strings. To force the transfer of RSF values to other VAMAS
blocks regardless of such constraints, use the button on the SNMS RSF
Calculator property page.

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Following these operations the VAMAS blocks in stainless steel sample ispopulated with RSFs from the Hastelloy standard. These values can beviewed via the Calibration property page, where the table lists both the RSF
per cycle and also the sputter rate per cycle. The remaining step is to assign asputter rate for the stainless steel sample using the Calibration property
page.

Specifying the Sputter-Rate
The sputter rate for a profile is updated on the Calibration property page of
the Dynamic SIMS dialog window. The information presented on the
Calibration property page is designed for calibrating dynamic SIMS profiles.
The mechanism allows the specification of sputter rates and RSFs based on
matrix materials. Since the RSF is already added to the SNMS data via the
Prepare Profiles or SNMS RSF Calculator property pages, the RSF must be
retrieved before applying the newly calculated sputter-rate to the SNMS
profile. Note that all VAMAS blocks in the row containing the block used toenter the sputter rate are also updated.
To update the sputter rate for a profile, perform the following steps using theCalibration property page.

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1.
2.
3.
4.

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Select an entry from the Matrix Index column as shown.
Press the RSF button to retrieve the RSF value from the table.
Enter the Crater depth in the text-field just below the Depth (nm)label before pressing the Compute Sputter Rate button.
Press the Apply RSF/SR to Matrix button.

Creating a Calibrated SNMS Profile
Once the set of VAMAS blocks containing the SNMS profile have been
populated with RSFs and the sputter-rate, quantification in terms of Atomic
or Mass concentrations is achieved by pressing the appropriate buttons on
the either the SNMS RSF Calculator property page or the Prepare Profile
property page.

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These two property pages provide a means of quantifying SNMS data either
one file at a time or multiple files in one operation.
The SNMS RSF Calculator property page provides a means of quantifying the
SNMS profile in the active tile. To perform the quantification step, display
one or more VAMAS blocks in the active tile. Ensure the RSF and sputterrates are correctly assigned for each of the VAMAS blocks by inspecting thetable on the Calibration property page. To quantify the profile, press the %Atomic or % Mass buttons on the SNMS RSF Calculator property page. A newexperiment frame is created containing a set of VAMAS blocks in which thedata are scaled by the sensitivity factors and offered as a percentage of thetotal scaled intensities. The profiles are therefore presented in the form of anamount of substance rather than the raw signal.
Before quantification the signal is displayed in raw counts against acquisition
cycle number.

After quantification, the data are presented in percentage of material against
depth in nanometres.

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The alternative to performing the quantification on a file by file basis is toprepare a set of SNMS profiles and then use the Prepare Profile property
page to quantify the data in one operation.
Sputter rates may be transferred to other profiles using the Prepare Profile
property page in an analogous way to the RSF mechanism.
When multiple VAMAS files are opened in CasaXPS and prepared withappropriate RSF and sputter-rates, the Atomic % by File button or the Mass %by File button may be used to quantify the profiles in each opened file forwhich at least one VAMAS block is selected and the active tile displays datafrom one profile in the file. The following steps lead to quantification for two
profiles.
1.
Tile the experiment frames within the CasaXPS main window

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Select one of the VAMAS blocks common to both profiles to bequantified and press the Select and Display Matching Blocks button.

3.

Deselect the VAMAS block in the experiment frame for which noquantification is required.

4.
5.

Press the Atomic % by File button.
Review the list of files displayed in the resulting dialog window andpress OK if all is well.
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Two new experiment frames appear containing the quantified profiles fromthe two files for which at least one VAMAS block is selected.

Note that:
Only files in which a VAMAS block is selected are quantified.
Each raw file contains the information required to perform thequantification and therefore any number of different files can bequantified at once provided the RSF and sputter-rates are prepare
appropriately and a selection includes at least one VAMAS block.
The Control-Key and the mouse can be used to add to the selection
across experiment frames, so the operation is not limited by thefunctionality of the selection options on the Prepare Profile property
page.
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Hiden SIMS/SNMS Workstation

Dynamic SIMSThe Dynamic SIMS technique etches a sample using an ion gun whilst
monitoring the signal for a set of isotopes. The resulting profile represents a
measure for the composition of the sample as a function of depth, where raw
data takes the form of counts per acquisition cycle as a function of
acquisition cycle time. These raw data are calibrated using the tools on the
Dynamic SIMS dialog window to provide profiles in terms of atomic density
plotted against depth in nanometres.

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Quantification of SIMS data is complicated by virtue of measuring theintensity of the secondary ions generated by the interaction of the primarybeam on the sample surface. The complexity results from the dependence ofthe signal intensity on the bulk properties of the sample. That is, a change inthe material etched by the ion beam may alter the signal intensity for thesecondary ions regardless of the concentration of the element within thesurface. It is therefore important to identify the essential structure of asample, referred to as the matrix material, with the understanding thatshould the matrix material change, both the signal intensity for mass peaks
may change as well as possible changes to the etch rate. SIMS analysis ishighly sensitive and ideal for the analysis of dopants, diffusion studies andcontamination. Quantification schemes for SIMS generally assume that the
impurity being measured is dilute (less than a few percent). Above this dilute
limit the probability of ionisation becomes dependent upon the impurity
concentration itself, as well as the chemistry of the matrix.

Notes on Dynamic SIMS RSF Calculation
Reference Signal Measured during the Course of Profile
Dynamic SIMS relative sensitivity factors (RSFs) are the means by whichmeasured implant signals are scaled to permit meaningful comparisons ofprofile data. During the course of a measurement, the signal may change fora variety of reasons and as a result a common practise is to measure both theimplant signal and also the matrix signal. The matrix signal provides theexperimental context for the implant signal, therefore the calculation of an
RSF from a standard sample includes the matrix signal measured in counts
per second. Since an RSF is essentially a scale factor and the matrix
monitored during the course of the profile is a sequence of measurement,
the value included in the RSF calculation is determined from an average ofthe matrix acquisition cycles.
An alternative to measuring the matrix signal at the same time as the implantis to monitor the matrix signal following the profile completion. The structureof the experiment changes slightly when the matrix signal is determinedfollowing the implant measurement, and since the RSF calculation for bothscenarios are generalised by the reference signal estimation following the110

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profile, the discussion of the RSF computation will be based on the moregeneral case.
Reference Signal Measured at End of Acquisition Cycles

d1

d2

Consider a sample created from a matrix material A implanted with amaterial B using a fluence φ atoms per cm2. If the resulting sample is profiledusing C data acquisition cycles followed by a matrix signal measurement,
where each acquisition cycle takes t seconds per cycle and the matrix signal ismeasured for a further T seconds resulting in a crater of depth d cm, then the
RSF for equivalent samples can be determined as follows.
The reference signal measured during the period T corresponding to the etchvolume characterized by the depth d2 is assumed to be representative of thematrix signal throughout the profiled volume characterized by the depth d1.
Further, the sputter rate is determined from the total depth of the crater
equal to d1+d2 divided by the total etch time. Hence d1 = td / (t+T). The RSF
for the given experiment is:
RSF

tCI A
1
I B I bg C d1

(1)

where
1. IA is the matrix signal in counts per second,
2. IB is the sum of the signal from the implant over the acquisition cyclesC

I i in counts,

IBi 1

3. Ii are the counts record for the implant in each cycle and4. Ibg is the background counts for the implant signal.
The formula for the RSF in Equation (1) is defined in terms of parameters
determined from an experiment. There are assumptions within this formula
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IA

(2)

1 C I i I bg
d1
C i1
t

The denominator in equation (2) is an approximation to the integral of the
background subtracted implant counts per second integrated over the depthof the profiled volume. That is:
d1

1 C I i I bg
C i1
t

d1

( I ( x) I bg )
t

0

(3)

dx

where the approximation in Equation (1) assumes a uniform step-size Δx =d1/C for a rectangular integration scheme. If the step-size as a function of
depth changes during a calibration profile, the RSF calculated from Equation(1) will be less representative of the measured uncalibrated implant dose.
Since the objective of calibrating an implant signal is to ensure that profiles
obtained from identical implantation conditions return identical areal
densities, or stated mathematically, integrals of the form in (3) for RSF scaled
intensities are all the same when calculated from profile data measured forsamples with identical implant dose, computation of the integral in Equation(3) is preferable to the summation in the same Equation. Therefore, the RSF
calculation in version 2.3.15 of CasaXPS is now performed using:RSF

I A d10( I ( x) I bg )
t

(4)
dx

Equation (4) better represents the nature of the dynamic SIMS RSF as ascaling factor for adjusting implant intensities relative to a known fluence φ.
The inclusion of the matrix signal IA in the RSF calculation is to allow the
implant intensity to be further normalised with respect to the matrix signal asa means of removing instrumental variations possible during the course of a
profile, or in the case of the reference signal at the end of the profile,
between different profile measurements.

Quantification of Dynamic SIMS Profiles
The options on the Calibration property page of the Dynamic SIMS dialog
window are designed to permit the analysis of samples for which the matrix
material changes in the course of the experiment. Although multilayer
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materials are analysed using dynamic SIMS, the typical sample consists of asingle matrix and one or two impurities appearing in dilute quantities
compared to the matrix. For this reason, the first perspective of theCalibration property page will be that of these more common and simple
samples.
Most data systems used to acquire dynamic SIMS profiles provide a means ofexporting the data in an ASCII format. These data files must be converted to
VAMAS format by CasaXPS using a very specific structure within the ISO
14976 definition. The experimental context for the dynamic SIMS profiles iscollected into a VAMAS file by CasaXPS and presented as a set of VAMAS
blocks. Each VAMAS block within a file manages the quantification
information in a set of corresponding variables (as specified by the ISO
format). The Calibration property page on the Dynamic SIMS dialog window
displays these corresponding variables in a table.

Data file supported by CasaXPS include:
1. Hiden Analytical Limited
2. Two formats for Cameca IMS instruments.
3. RBD Instruments Inc. PHI-upgrade system.
To convert a native ASCII format to VAMAS format suitable for quantificationin CasaXPS, convert the data using the Convert option on the File menu or
the Convert toolbar option.

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Quantification of Basic Profiles
An example based on Cameca IMS-6f old ASCII format.
Converting Cameca Depth Profiles
Depth profile data from Cameca IMS-6f SIMS instruments can be exported via
ASCII formatted files. These files, when written to disk, are assigned a fileextension of .dp_ascii and, if exported from the raw data, include
experimental parameters plus two columns of X/Y pairs representing the
etch-time per cycle and the secondary ion intensity in counts per second.

CasaXPS will convert these .dp_ascii files only when the raw data is exported.
Conversion is performed using the Convert option on the File menu or via thetoolbar button. A File dialog window is invoked by these options, in which the.dp_ascii file containing the raw data is selected and the Open buttonpressed.

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A new VAMAS file will be written to the same directory containing theoriginal ASCII data after which the profile appears in a new experiment framein CasaXPS.

When more than one profile is of interest, the data can be combined into asingle experiment frame via the Convert and Merge option on the File menu.

Again a File dialog window appears, in which each .dp_ascii file within thecurrent directory can be selected using the mouse and the Control Key; onpressing the Open button on the dialog window the entire set of selected
dp_ascii files are converted to VAMAS files and the resulting files loaded intoa single experiment frame.

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The directory containing the original dp_ascii files will also containcorresponding VAMAS files. Since the conversion process involves writing
new VAMAS files, it is important that the directory containing the data musthave write permission and there is sufficient space on the disk to receive the
new VAMAS file.
Quantification Information
After conversion to VAMAS format, both the timing information and theintensity units are adjusted to those used internally by CasaXPS. Most
notably, the intensity unit in the .dp_ascii file is counts per second, however
the intensity in the VAMAS file will be measured in counts per cycle and theabscissa becomes cycle index. All the associated timing information is also
save with these abscissa and ordinates so that the calibration to depth andatomic density can be computed later.
Mass channels used to measure the secondary ion intensity are labelledwithin the .dp_ascii file using the nominal mass and the element nameabbreviation. When entered into the VAMAS file, the block identifier isassigned the original string used to label the mass channel, however CasaXPS
attempts to extract the nominal mass and the element abbreviation for use
in the element and transition fields used by the VAMAS format. The
concatenation of these element and transition fields provides theinformation used to align the VAMAS blocks within the experiment frame andis also used to determine the isotopic abundance ratio, which in turn is used
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element/transition fields for a profile are not correctly assigned, should theuser request elemental sensitivity factors an error message will result. In theevent that the element and transition fields do not contain the element andisotopic information required to determine the relative abundance for an
isotope, then these fields must be edited to reflect the true isotope used tomeasure the profile. To edit these fields:
1.
Select the VAMAS block(s) in the right-hand pane of the experimentframe.
2.
Press thetoolbar button and, on the resulting dialog window, enter
the correct element abbreviation and nominal mass for the isotope of those
VAMAS blocks in the selection.
When the information on the dialog window is accepted, the VAMAS blocks
in the right-hand pane of the experiment frame are re-organised to reflect
the new assignment.
One way to check the possible values for the element/transition entries is to
use the Exact Mass Calculator property page on the Element Library dialog
window.

Enter a string such as “Si28” into the text-edit field on the Exact Massproperty page and press return or the Add Formula button. If a valid isotope
string has been entered, then the string will be entered into the scrolled list
above the text-field. Otherwise, an error dialog indicated an error occurred. If
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elemental RSF values are desired, it is important the string above the VAMAS
block in the experiment frame is accepted by the exact mass calculator;
acceptance of a string indicates the database includes the informationnecessary for the conversion of the RSF.
Calculating Relative Sensitivity Factors for Simple SIMS Measurements
Quantification of dynamic SIMS profiles is based on determining absolutescaling factors, which when applied to the profile data convert the raw signal
into atom density measured in atoms per cm3. Determination of these RSFs
requires the measurement of a profile from a material of known
composition. For dynamic SIMS, known composition means knowledge of thematrix material and the impurity implant dose used to prepare the standard.
The example used to illustrate the process for calculating an RSF is gallium
implanted with silicon (dose = 2e14 atoms per cm2, crater depth = 1776.4
nm). The profile measured on a Cameca IMS-6f includes the isotopes Ga 69
and Si 28.

The following steps lead to calibrated depth and intensity scales for the datain the original .dp_ascii file.
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1. Convert the .dp_ascii file using the Convert option on the Filemenu.
2. Display the 69Ga data in the active display tile
3. Left-click on the active tile to enable the toolbar buttons.

4. Invoke the Dynamic SIMS Calibration dialog window by pressing the
Dynamic SIMS toolbar button.

The top left-most text-field displays the Block Id for the data which is thecurrent focus of the Dynamic SIMS dialog window.

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5. Press the Define Matrix button.
Provided no cycles are selected in the scrolled list below the Define Matrix
button, a dialog window indicates that no selection is active and asks
whether all cycles should be updated for the profile in the active tile.
6. Press the Yes button and observe that the Matrix Index column ofthe scrolled list is updated with the string 69Ga.

If a cycle selection has been made within the scrolled list, then all cycles must
be selected before pressing the Define Matrix button is pressed.
The second column in the scrolled list is labelled Interface. For this particularprofile, the same matrix is present throughout the etch cycles and therefore
the use of the Interface column is unnecessary. If the material were amultilayer sample, where RSF and sputter-rates varied between layers, then120

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the Interface column would need to be populated with strings corresponding
to the different materials characterising the layer structure. Once the layers
are established, the Interface definition allows the assignment of RSF andsputter-rates to the individual layers.
7. Double-click on the 28Si VAMAS block so that the silicon profile isdisplayed in the Active Tile.

8. Press the Define Surf/BG button.
Two regions are created on the 28Si profile and these mark the surface limit
and the background to the secondary ion signal.

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Adjustments to these regions are performed using the Quantification
Parameters dialog window.
9. On the Calibration property page, enter the crater depth value
measured for the standard (crater depth = 1776.4 nm)

10.Press the Compute Sputter Rate button.

11.On the Calibration property page, enter the dose value known forthe standard (dose = 2e14 atoms per cm2)

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12.Press the buttons labelled Compute RSF

13.Select one cycle in the scrolled list on the Dynamic SIMS dialog
window and press the Apply RSF/SR to Matrix button.

The values from the two text-fields for the RSF and the sputter-rate will beentered into the corresponding fields in the scrolled-list for each cycle forwhich the matrix index is identical to the one previously selected.

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14.Press the button labelled Calibrate Depth Profile.

The RSF and sputter-rate entered into the 28Si table are used to compute theatomic density and the depth; the computed profiles are entered into a newexperiment frame.

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The new experiment frame contains a VAMAS block for each VAMAS block in
the original file. Within these new VAMAS blocks, several corresponding
variables are defined which are assigned values for the intensity in counts per
second plus the RSF and sputter-rate used to calibrate the profile. These
values can be viewed using the Crtl PageUp/Crtl PageDown mechanism forstepping through the corresponding variables in a VAMAS block.
NB: To compute the elemental RSF from an isotope profile, the tick-box
labelled Elemental RSF must be ticked and the element/transition field for
the VAMAS block in use must be set appropriately.
Making Adjustments to the Sputter Rate
A depth profile prepared for calibration must have an RSF and sputter rate
defined for each matrix within the analysis volume. If at a later time it isdesired to alter the RSF or sputter rate for a given matrix, the following
sequence of steps should be used:
1. Select a cycle from the scrolled-list to identify the matrix for which
the RSF or sputter-rate requires adjusting.
2. Press the pushbutton labelled Restore RSF/SR.

The values for the matrix identified by the chosen cycle are entered into thecorresponding text-fields for the RSF and Sputter Rate on the dialog window.
3. Either the RSF, the sputter rate or both the RSF and the sputter rate
can be recalculated before again pressing the Apply RSF/SR toMatrix button. The matrix defined by the selected cycle will be
updated with the modified values.
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Display of Calibrated Profiles
The labels for identifying the x and y axes in a display tile are determinedfrom the first VAMAS block with respect to the order of selection in the righthand pane of the experiment frame at the time the VAMAS blocks areoverlaid in the display tile. If a row of VAMAS blocks are selected by clicking
on the experimental-variable value for the row, then the left-most VAMAS
block will determine the axes labels. Matrix signals are typically notcalibrated and in the event the first VAMAS block contains the matrix signal,
the profile would appear with the y-axis displaying an arbitrary scale.

When calibration is performed, only those profiles for which quantification
information is supplied are converted to atom density. Profiles with an RSF ofunity are scaled to ensure the profiles appear within the range for thecalibrated profiles; hence the y-axis label is assigned the string “Arbitrary
Units”. To display an overlay of the profiles where the Y axis is labelled withrespect to a calibrated profile, namely “Atomic Density”, it is necessary that acalibrated VAMAS block is selected first. To select VAMAS block in anarbitrary order, left-click the first VAMAS block, then hold the Control Key
down and left click the other blocks required for the display. The traces are
displayed in the active tile by pressing the overlay toolbar buttonordered with respect to the selection sequence.
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The VAMAS block for the impurity 28Si is selected before the matrix 69Ga.

Further Aspects of Dynamic SIMS Quantification
Logical Structure of a SIMS Depth Profile within CasaXPS
A depth profile is a collection of VAMAS block all assigned to the same
experimental variable value; typically the experimental variable will be anindex number for a given file of data. There may be more than one profile per
VAMAS file, where each profile will occupy a row as viewed via the right handpane of the experiment frame.

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For each VAMAS block within a raw depth profile, a number of corresponding
variables are setup to offer fields for use in the quantification step. The
important fields for quantification are displayed in the Matrix Index table on
the Calibration property page of the Dynamic SIMS dialog window.

Methods for Computation of RSF and Sputter Rate Values
RSF values are computed from standard materials using one of three
approaches:
1. Matrix, dopant and crater depth.
2. Matrix, known bulk doped atomic density and crater depth.
3. Interface assignment with respect to depth and atomic density.
The computation of the RSF requires the determination of values from theMatrix signal and also the Implant. To support the determination of thesequantities the matrices within a profile must be identified and a pair ofregions defined to specify the surface zone as well as the appropriate
background signal for a given mass.
Identification of the Matrix and Interface Cycles
Defining the matrix for experiments involving a Single matrix material isachieved as follows:
1. Display the matrix signal for each profile in the active display tile.
2. Press the Define Matrix button on the Calibration property page on
the Dynamic SIMS dialog window.
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A pop-up window will inform you that no matrix index is selected and asks
whether the displayed matrix should be applied to all Cycles. Answer bypressing the Yes button. To avoid the warning message, before pressing theDefine Matrix push button, first select all the table entries by pressing theheader button for the column labelled Matrix Index. If there are any rows
currently selected it will be necessary to de-select these rows before pressing
the header Matrix Index.
If the file contains more than one depth profile and the matrix for eachprofile is overlaid in the active tile, then the operation of defining the matrix
for each depth profile is performed in one go.
Defining the matrix for Layered materials is achieved as follows:
A key point for SIMS is that the signal from a given mass peak depends on theenvironment in which the isotope is found. As the crater bottom moves
through an interface between differing materials there is potential for both
the relative sensitivity and the etch rate to change during the course of theacquisition. The example used to illustrate a layered material involves
profiling magnesium in gallium with an aluminium layer in the form of GaN :AlGaN : GaN (Dr Shadi Shahedipour, University of Albany, New York).

The secondary ion yield for Mg differs between the GaN and the AlGaN
layers. Presentation of these types of samples requires a means of adjusting
the Mg RSF for acquisition cycles depending on the aluminium signal
strength.
The table on the Calibration property page provides two columns headed
Matrix Index and Interface. These columns specify the matrix material and129

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also structures within the profile where the RSFs for a given isotope change
due the material environment rather than changes to the atomic density. The
procedures for defining the matrix and also a layer are identical except fordifferent buttons are used to make the assignment. For the current example,
the Ga2 signal is most representative of the gallium matrix, while the Al signal
best defines the interface between the GaN and AlGaN layers. The matrix
signal Ga2 is common to both layers therefore the Ga2 profile can be definedas the matrix throughout the profile:
1. Display the Ga2 VAMAS block in the active tile.

2. Ensure the Matrix Index column of the table on the Calibration
property page is either all selected or none are selected before
pressing the Define Matrix button.

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All VAMAS blocks from the same row in the right-hand pane will now show
the same Ga2[2] matrix for each cycle throughout the profile.
At this point the Interface column is populated with the 69Ga[0] reference,that is, the matrix and interface columns are initialised to the first VAMAS
block in the file. Only the matrix has so far been replaced by a reference to
the Ga2[2] VAMAS block. Since the depth profile includes two environmentsfrom which the Mg signal is measured, to distinguish between these twoenvironments the cycles corresponding to the AlGaN layer must be identified.
The Al signal provides the means of specifying the appropriate set of cycles
for which AlGaN is significant compared to the GaN layers.
1. Display the signal for Al in the active display tile.

2. Either using the table or the mouse (see below), select ranges of cycles
within the Matrix Index column of the table on the Calibration property
page.

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3. Press the Define Interface button. Only those cycles selected in thetable will be assigned the VAMAS block reference Al[1].

Selecting Ranges of Cycles on the Calibration Property Page
Selecting rows within the Matrix Index table is achieved using the table
together with the Shift and Control Keys. Alternatively, the selection can be
defined using the active tile and the mouse. When the Shift Key is held down
and the left mouse button is used to drag over the display, the set of cycles
corresponding to those lying between the vertical cursors will be selected in
the Matrix Index table.

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The use of the cursor and Shift key aids the identification of layered
structures viewed via a profile signal. Once a set of layers are so indicated,
the assignment is made by pressing the Define Matrix or Define Interface
button, as appropriate.
Surface Data and Background Signal
Since SIMS signal intensity depends on the matrix material, adventitious
carbon or other surface contaminants may result in signal from the surface
deviating from the bulk behaviour. It is therefore sometime appropriate to
exclude surface acquisition cycles from the RSF determination. Further a bulk
material may also cause a residual signal for the implant and therefore
removal of a background count rate is also appropriate. To aid thespecification of these two limitations when calculating RSF values, tworegions must me defined for each VAMAS block before an RSF can becomputed.
Defining the Surface and Background Regions:
1. Display any number of VAMAS blocks in the active display tile.
2. Press the Define Surf/BG button.

Two regions will appear on each profile; the left most region indicates thepeak and should be adjusted to start just after cycles associated with any
surface spike. The second right-most region defines the background to thetail of an implant. Both regions can be adjusted using the Quantification
Parameters dialog window when viewing the Regions property page. The left
mouse button may be used to drag the start and end position of theseregions whenever the Region property page is active. Adjustment undermouse control is available when grey vertical lines at either end of theregions are displayed which appear when the Region property page is topmost on the dialog window.
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Three Ways to Calculate RSF Values from Standard Samples
Once the matrix and regions have been defined, the RSF can be computed by
the appropriate method:
Either: enter the Implant dose in Atoms/cm2 and the measured crater
depth in nanometres then press the Compute Sputter Rate button
before pressing the Compute RSF button. Pressing these buttons will
result in the corresponding values appearing in the boxes below the
buttons.
Alternatively, if a bulk doped standard is in use, tick the box labelled
Use Bulk Doped and enter the known atom density into the above
data input field. When a bulk doped standard is used to compute the
RSF, both the implant and matrix require regions.
The third method for computing the RSF is via a known implant depth
and atom density. The button to the right of the Depth field, namely,
results in a dialog window in which a depth and/or apeak intensity can be entered. The position of the implant is definedusing the Matrix Index table by making a single selection in that table.
The appropriate cycle can be identified by left-clicking on the peak in
the left-hand pane active tile. The Matrix Index table scrolls to show
the cycle corresponding to the mouse selection and the table entry is
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therefore offered for selection prior to invoking the Define Depth byCycle dialog window. If the correct depth and corresponding atoms per
cm3 are entered, the Calc RSF tick box is ticked and the OK button ispressed, the RSF, Depth and Sputter Rate fields will be updated.

Adding RSF and Sputter Rates to Profile Data
Once an RSF is computed and the appropriate Sputter Rate entered for an
implant in a given matrix, the profile can be update with these values: selecta cycle from the Matrix Index table with the appropriate matrix entry andpress either the
button or the
button.
Each cycle within the profile with the same entry as the selected matrix index
will be updated with both the Sputter Rate and the RSF. If the material is amultilayer structure the procedure should be repeated for each layer, where
the RSF and Sputter Rates are first determined from a standard profile. An
RSF/Sputter Rate pair can be extracted from another profile by firstdisplaying the profile, making a selection in the Matrix Index table andpressing the
button. The RSF/Sputter Rate from the indicatedmatrix index will be entered into the fields on the dialog window, thus
allowing the unknown to be subsequently displayed and these restored
values from the standard used to update the unknown profile. Note, theDose and depth for single matrix material are computed when the button
Apply to Selected Matrix is pressed.
Applying Calibration Parameters to One or More Profiles
Once RSF and Sputter Rates have been assigned to each depth profile, thedata are calibrated by pressing the Calibrate Depth Profile button. If multiple
profiles are prepared and overlaid in the active tile, pressing the Calibrate All
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entered into a single experiment frame. The depth scale units must be
selected prior to calibration using the tick box Use Nanometres.
Note: If normalization to the matrix is not requires, it is necessary to compute
the RSF with the same selection of the Normalize tick box.

Depth Profile Statistics: Areal Density and Decay Length
Areal Density and Decay Length are computed as part of the Depth Profile
Statistics. The procedure for calculating these statistics requires a pair of
cursors to be defined on the displayed profile in the active tile. The aim is tomark the region over which the profile peak appears. To mark the cursors on
the profile: hold the Shift Key down and drag a box starting from the left ofthe peak and ending at the right-hand end with the mouse positioned at theintensity of the background. On pressing the Profile Statistics button a dialog
window appears showing the current text in the VAMAS block comment plus
a set of lines offering the new calculated profile statistics. If it is desired toinclude these new lines in the VAMAS block comment, then the OK button
should be pressed, otherwise the Cancel button will exit without altering the
VAMAS block comment. Note, the text in the VAMAS block comment can beedited within this window leaving only the information so required.

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Maintaining Standards Library Files
Once standards have been prepared and RSF/Sputter Rates computed, these
depth profiles can be moved to other files containing profiles from standards.
The toolbar buttons
allow VAMAS blocks to be copied into an
existing file and also delete from a file. If a number of standard material
profiles are located in a single file, thebutton offers a means ofsearching the strings within a VAMAS block comment and those matched areboth selected in the right-hand pane of the experiment frame and are also
displayed in the scrolled list of display tiles. VAMAS block comments can beedited using thetoolbar button.

Step-by-Step Description of Quantification for a Multi-Layer
SampleIn this example, the desired result is to plot atomic density verses depth for
Mg implanted in Gallium. To achieve this end and owing to the layered
structure, four masses were monitored, where two labelled 69Ga and Al
define the layer structure while the trace labelled Ga2 represents a constantmatrix signal, to which the Mg signal is normalized.
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Step 1: Define the Matrix
Display the matrix VAMAS block, namely, Ga2 in the activetTile. The block id
plus the VAMAS Block index for the trace will appear on the Calibration
property page of the Dynamic SIMS dialog window.

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Select all the cycles under the Matrix Index column in the table on the
Calibration property page and press the Define Matrix button; the selected
entries under the Matrix Index column will change to Ga2[2], thereby
showing the matrix is defined.
Step 2: Define the Layer Structure
The structure of the material is GaN : AlGaN : GaN (Dr Shadi Shahedipour,
University of Albany, New York) therefore the matrix definition alone is not
sufficient to specify the cycles for which different sputter rates and RSF must
be assigned. Thus a sample such as this one requires the definition ofquantification information using the interface column within the table on the
Calibration property page. The AlGaN layer is characterized by the tracelabelled Al. To define a layer within the profile, the signal Al is used to selectthe set of cycles recorded between the two interfaces.

Before using the mouse to indicate the interfaces, ensure there are no
selected cycles in the table on the Calibration property page. Clicking on any
column away from the Matrix Index column will de-select all cycles. Note,
repeated use of the mouse will add to the current selection, allowing
complex multilayer materials to be specified. Mark the AlGaN layer byholding the Shift-Key down and then dragging a box from the left to the right139

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Copyright © 2010 Casa Software Ltdof the AlGaN peak. The result of such an action is shown in above. All thecycles within the table on the Calibration property page between the verticalcursors shown above are selected by the mouse action and so pressing theDefine Interface button on the same property page will cause the Interface
column in the table to be updated.

Step 3: Enter RSF and Sputter Rate Values
In this example the RSF and Sputter Rate for the two layers are assumed tobe known. All that is required is to add sputter rates and RSF for each of thethree layers; the values are entered on the Calibration property page. The
required information for quantification are two RSF and SR pairs, which must
be entered correspondingly for the GaN and AlGaN layers. Since the matrix
does not define the layer structure, the assignments are made by using the
Apply RSF/SR to Interface button. After displaying the Mg trace in the active
tile the RSF and sputter rate for each layer can be entered in turn. Since theInterface column was initially all assigned 69Ga[0], the layer assignment
based on the Al signal only altered the range of cycles specified by thevertical cursors. As a result the GaN layers are identified by the Interface
entries 69Ga[0]. Thus, both the GaN layers are assigned RSF and sputter rates
by selecting one cycle for which the interface column contains 69Ga[0],entering the appropriate RSF/SR and pressing the Apply RSF/SR to Interface
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button. Each cycle previously designated as part of the 69G [0] layer will
receive the RSF/SR pair.

Similarly, the AlGaN RSF/SR values are entered in the text-fields, one cyclewith an Interface column of Al[1] selected and the Apply RSF/SR to Interface
button pressed a second time. Again, each cycle designated as Interface Al[1]will receive the RSF/SR pair.

Step 4: Calibrate Mg Profile
Calibration is performed by displaying the Mg profile in the active tile andpressing the Calibrate Depth Profile button.
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In this example, the only mass for which RSF/SR pairs are entered is Mg. The
SR are automatically assigned to all masses, however the RSF values formasses other than Mg remain set equal to unity. A consequence of leaving an
RSF equal to unity is that on Calibration to atomic density and depth, masses
for which the RSF is equal to unity will be scaled to the atomic density rangeof any properly calibrated masses. This allows an overlay with respect to thecalibrated traces, without requiring the RSF for all masses to be assigned
prior to calibration. Counts per second traces are available in the calibrated
experiment frame as the second corresponding variable (Ctrl PageUp/Crtl
Page Down).

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An Example of Computing an RSF using Dose and Implant Peak
Depth
A profile was obtained from GaN undoped epi growth ion implanted with24
Mg at a dose of 1.0e15 atoms per cm2. The depth at the peak of the Mg
counts is 77 nm. Computation of an appropriate RSF is performed as follows:

Step 1: Define the Matrix
Display the Ga2 matrix profile in the Active Tile, press the header buttonlabeled Matrix Index in the table to select all cycles and press the Define
Matrix push button on the Calibration property page. The table on the same
property page will update to show that the Matrix index for each cycle is now
assigned to the Ga2 profile.
Step 2: Define the Surface Layers and also the Background for the Mg
ProfileDisplay the Mg profile in the active tile and press the button labeled Define
Surf/BG. Two regions are created on the Mg profile. The left-most end of theleft-most region defines the surface layers, while the background to the rightmost of the two regions estimates the background to the Mg signal.

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Step 3: Define the Depth Scale
In this example, the depth scale is defined to be 77nm at the maximum signal
for the Mg profile. Using the left-mouse button, click on the profile toindicate the position of the Mg maximum values. The table entries on the
Calibration property page will scroll so that the cycle corresponding to theposition of the vertical cursor, which is located at the top of the visible
portion of the list. Select the entry at the top of the visible portion and press
the button next to the Depth (nm): label. A dialog window appears in which
the selected cycle index in already entered and a text-field for the Depth(nm) corresponding to the indicated cycle can be input.

On pressing the OK button, the Calibration property page is updated with thedepth computed from the Define Depth by Cycle dialog window values.
Step 4: Enter the Dose and Compute the RSF
Enter the dose in atoms per cm2 on the Calibration property page and press
the button labelled Compute RSF. If the elemental RSF is required, the tickbox just above the Compute RSF button should be ticked.
Step 5: Calibrate the Mg Profile
Once the RSF is computed and the sputter rate updated, the values for eachcycle corresponding to the Mg profile (currently displayed in the active tile)
must be updated. In this example, the assignment for the matrix is sufficient
to target the cycles for which RSF and sputter rates must be applied. Simply
select any cycle using the Matrix Index column in the table and press the
Apply RSF/SR to Matrix button. Since all the cycles are defined to have thesame matrix, the table for the Mg profile will contain values for the RSF andsputter rate throughout. To calibrate the profile, press the button labelled
Calibrate Profile.

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Note that the Profile Statistics button has been used to create a VAMAS
block comment showing the Areal Density and Decay Length for the Mg
profile. Also note how the profiles for which no RSF is specified are scaled toallow their visualization within the same scale as the calibrated Mg profile.

Computing RSFs where the Matrix Signal is Measured following
the Completion of the Implant Profile
Cameca dynamic SIMS instruments permit experiments in which only the
implant is profiled. The inclusion of the matrix intensity in the computed RSF
is achieved by measuring the matrix signal after the implant signal attenuates
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to background levels. The assumption is therefore that the matrix count rateis constant during the acquisition of the dopant profile. While in principle theCameca files contain the experimental parameters for the profile, there areoccasions where the matrix reference signal must be inspected and manuallyentered. To calculate the RSF for a standard material based on an implant
profile only, the following features are employed.
The VAMAS file for a single boron implant in silicon consists of a single
VAMAS block.

Following the measurement of the boron profile, the Cameca monitors thematrix signal, and records the counts per second for the matrix in the data
file. It should be noted that the crater depth measured following such an
experiment includes the depth etched during the matrix measurement which
occurs after the boron profile is completed.
Calculation of the RSf for 11B implanted in silicon is computed identically toprevious examples with the exception that the user inputs the matrix signal
in counts per second via the Ref Signal button on the Calibration property
page. The VAMAS block containing the boron profile is updated with theintensity of the matrix signal via the Reference Signal dialog window invokedby the Ref Signal button.

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Computing the RSF is performed as follows:
1. Enter the crater depth (770 nm) and press the Compute Sputter Rate
button.
2. Enter the dose (5x1014 atoms per cm2).
3. Check that the reference signal is correctly assigned and enter thecorrect value by pressing the Ref Signal button.
4. Press the Compute RSF button.

Gathering Profile Data for Display and Calibration
PurposesProfile data typically is stored as individual VAMAS files. There are however
reasons why merging these files into a single experiment frame is desirable.
For example, data can only be overlaid for display purposes for data locatedin the same experiment frame. A further reason for moving profiles into asingle experiment frame is that Calibration of a dynamic SIMS profile isperformed on the Calibration property page and the button for calibrating
multiple profiles only acts on data within a given experiment frame. Copying
profiles into a single experiment frame permits many profiles to be calibrated
in one action.
By way of example, consider merging two VAMAS files containing profile data
for which a display of the data in overlay format is required.
1. Open each of the two data files in CasaXPS.
2. Using the Window menu, tile the two experiment frames so that bothright-hand panes are visible such that the VAMAS blocks are easily
selected.
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3. Create a new experiment frame
blocks toolbar button.

and press the Copy/Paste VAMAS

4. Check that the VAMAS blocks listed on the Copy Selection dialog
window match those selected in the two files and press the OK button.
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The selected VAMAS blocks now appear in the new experiment frame. Notethat the selected VAMAS blocks are transferred to the experiment frame withfocus. In the event that the experiment frame with focus already contains
VAMAS blocks the selected VAMAS blocks are appended to the existing
blocks. The target experiment frame for this example was initially empty
therefore only the selected blocks appear in the experiment frame.

5. Save the new experiment frame to disk.
After preparing the profiles with appropriate RSFs and sputter rates theentire set of profiles is calibrated by overlaying the implant VAMAS blocks inthe active tile and pressing the Calibration All Profile button.

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A new experiment frame appears contain the quantified profiles.

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