DS-11 Series
Spectrophotometer / Fluorometer

User Guide

Version: 9-MAY-2024
1

Table of Contents
1.

Introduction --------------------------------------------------------------------------------------------------- 6
Product Technology............................................................................................... 6

Upgrade Options ................................................................................................... 6
2.

Set up and Safety -------------------------------------------------------------------------------------------- 7
Cautions ................................................................................................................ 7
Instrument Rear Panel........................................................................................... 7
VCCI (Class B) compliance statement for users in Japan..................................... 83.

Instrument Diagram ---------------------------------------------------------------------------------------- 9

4.

Software Quick Guides ---------------------------------------------------------------------------------- 10
EasyApps

Software Icons ................................................................................ 10

Software Buttons ................................................................................................. 11
Software Navigation ............................................................................................ 11
Top Bar Overflow Functions ................................................................................ 125.

Absorbance Run Screen -------------------------------------------------------------------------------- 13
Run Screen.......................................................................................................... 13
Microvolume Measurements ............................................................................... 13

Cuvette Measurements ....................................................................................... 14
AutoRun............................................................................................................... 14
Measurement Modes ........................................................................................... 14
21 CFR Mode Measurements ............................................................................. 15
6.

Absorbance Report and Graph Screens----------------------------------------------------------- 16
Report Screen ..................................................................................................... 16
Graph Screen ...................................................................................................... 16

7.

Absorbance Best Practices ---------------------------------------------------------------------------- 18
Best Practices for Absorbance Measurements ................................................... 18

8.

Tech Team Tips -------------------------------------------------------------------------------------------- 19
Initialization .......................................................................................................... 19
Connectivity and Results Data ............................................................................ 19
Software Updates ................................................................................................ 19
Technical Support................................................................................................ 199.

Absorbance Nucleic Acid Apps ---------------------------------------------------------------------- 20
Quick Protocol ..................................................................................................... 20
dsDNA, RNA and ssDNA .................................................................................... 21
Microarray............................................................................................................ 22
Dye List................................................................................................................ 23
Baseline Correction for Dyes ............................................................................... 24
Nucleic Acid Concentration Calculations ............................................................. 25
Purity Ratios ........................................................................................................ 25

10. Absorbance Purified Protein, Peptide Apps ----------------------------------------------------- 27
Quick Protocol ..................................................................................................... 27
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Protein A280 ........................................................................................................ 28
Protein Type List.................................................................................................. 28
Baseline Correction ............................................................................................. 29
Labeled Proteins.................................................................................................. 30

Protein Type List.................................................................................................. 30
Dye List................................................................................................................ 31
Peptides............................................................................................................... 31
Protein and Peptide Concentration Calculations ................................................. 32
11. Absorbance Colorimetrics App----------------------------------------------------------------------- 34

Quick Protocol ..................................................................................................... 34
Generating a Standard Curve.............................................................................. 34
Line Fit ................................................................................................................. 36
Saving a Standard Curve .................................................................................... 36
Editing a Standard Curve .................................................................................... 36
Exporting a Standard Curve ................................................................................ 37
BCA ..................................................................................................................... 38
Bradford ............................................................................................................... 38
Lowry ................................................................................................................... 38

Pierce 660 ........................................................................................................... 38
12. Absorbance UV-Vis App -------------------------------------------------------------------------------- 39
Quick Protocol ..................................................................................................... 39
Wavelength List ................................................................................................... 39
Wavelength Range Selection .............................................................................. 39

Cursor Position .................................................................................................... 39
Baseline Correction ............................................................................................. 40
13.

Absorbance OD 600 App ------------------------------------------------------------------------------- 41
Quick Protocol ..................................................................................................... 41
Unique Features .................................................................................................. 42

14.

Absorbance Kinetics App ----------------------------------------------------------------------------- 43
Quick Protocol ..................................................................................................... 43
Define Method Screen Features.......................................................................... 43

15. Absorbance Custom Methods Apps ---------------------------------------------------------------- 47

Quick Protocol ..................................................................................................... 47
Primary Settings .................................................................................................. 48
Custom Standard Curve Methods ....................................................................... 48
Custom Formula Methods ................................................................................... 49
Formula Guidelines ............................................................................................. 50

16. Fluorescence: Basic Operation----------------------------------------------------------------------- 51
Fluorescence Measurements .............................................................................. 51
Best Practices...................................................................................................... 51
17. Fluorescence: Standard Curve Method Apps --------------------------------------------------- 53
Quick Protocol ..................................................................................................... 53
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Run Screen- Assay and Curve Selections .......................................................... 55
Run Screen- Standard Curve View ..................................................................... 56
18. Basic Fluorometer App ---------------------------------------------------------------------------------- 59
Quick Protocol ..................................................................................................... 59

19. Data Export and Print Options ------------------------------------------------------------------------ 61
Export Options ..................................................................................................... 61
Export Via Email .................................................................................................. 61
Export to a Network Folder .................................................................................. 62
USB ..................................................................................................................... 62

Print Options ........................................................................................................ 62
20.

Utility Apps and Functions ---------------------------------------------------------------------------- 63
User Accounts App .............................................................................................. 63
Data App.............................................................................................................. 65
Exporting and Deleting Data................................................................................ 65
Settings App ........................................................................................................ 66
Updater App ........................................................................................................ 69

21.

21 CFR App ------------------------------------------------------------------------------------------------- 70
Compliance Ready Software ............................................................................... 70

Activation Wizard Overview ................................................................................. 71
Activation Wizard 1/7 - Administrator Account .................................................... 71
Activation Wizard 2/7 – Enter Activation Code .................................................... 71
Activation Wizard 3/7 - Roles .............................................................................. 71
Activation Wizard 4/7 – Signature Meaning......................................................... 72

Activation Wizard 5/7 – Role-Signature Meaning Linking.................................... 72
Activation Wizard 6/7 – Password Rules ............................................................. 73
Activation Wizard 7/7 – Existing Users ................................................................ 73
Measurements and Electronic Signed Records .................................................. 74
Audit Trail ............................................................................................................ 75
Archiving .............................................................................................................. 76
22.

21 CFR Mode - Utility Apps and Functions ------------------------------------------------------ 77
User Accounts App .............................................................................................. 77
Data App.............................................................................................................. 79

Settings App ........................................................................................................ 80
Updater App ........................................................................................................ 80
23. Lab Tool Apps ---------------------------------------------------------------------------------------------- 81
Calculator App ..................................................................................................... 81
Timer App ............................................................................................................ 82

ScreenLocker ...................................................................................................... 82
24. Maintenance------------------------------------------------------------------------------------------------- 83
Cleaning .............................................................................................................. 83
Guidelines............................................................................................................ 83
Cuvette and Fluorescence Mode Holder Cleaning .............................................. 83
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Solvent Compatibility ........................................................................................... 83
25. Diagnostics -------------------------------------------------------------------------------------------------- 84
DS-11 Self Test ................................................................................................... 84
Lamp Reset ......................................................................................................... 84

Microvolume Pathlength Verification ................................................................... 84
Results................................................................................................................. 85
FX- Diagnostics ................................................................................................... 87
26. Troubleshooting ------------------------------------------------------------------------------------------- 88
Quick Help ........................................................................................................... 88

Software Errors.................................................................................................... 89
Printer and Barcode Scanner .............................................................................. 89
27. Customer Support ---------------------------------------------------------------------------------------- 90
Warranty .............................................................................................................. 90
Disclaimer ............................................................................................................ 90
Instructions for Disposal of Packaging and Waste Equipment ............................ 90
Research Use Only ............................................................................................. 90

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1. Introduction
Product Technology
DeNovix Spectrophotometers / Fluorometers are compact, stand-alone instruments witha high-resolution touchscreen. EasyApps software utilizes application specific icons
along with a custom operating system to provide an intuitive, easy-to-use instrument for
both absorbance and fluorescence measurements.
SmartPath technology automatically adjusts the microvolume mode pathlengths toenable sample measurements across a broad concentration range. Bridge Testing
verification identifies and adjusts in real-time for a broken sample column, ensuring
accurate measurements of difficult to pipette, low surface tension samples like proteins.
Absorbance range specifications are published on the DeNovix website.
FX models include a fluorescence mode while the DS-11+ and DS-11 FX+ instruments
also enable cuvette-based measurements for low concentration samples and basic
absorbance kinetic studies.

Key Features• Stand-Alone Design, no-PC Required• Hi-Definition 7-inch Touchscreen Interface• Simple, Intuitive EasyApps Software• 1 μL and Cuvette Full Spectrum UV-Vis Analysis• Four LED Excitation Options• Wi-Fi, Ethernet and USB connectivity

Upgrade Options•

Add the USB connected FX Fluorometer Module to enable fluorometer measurement
applications. Compatible with DS-11, DS-11+ and DS-C Spectrophotometers•

Activate 21 CFR Part 11 Compliance Ready Software.

62. Set up and Safety
1. Remove all packing materials.

2. Plug the unit into a 100-240 VAC, 50-60/Hz receptacle using the grounded power
supply (Globtek part number TR9CE3000C95CP-NR6B / RoHS Compliant) included witheach unit. Input Rating: 100-240V~, 50-60 Hz, IEC 60320/C14 , Output Rating: 36W,
12V@3A
3. Turn on the power switch located in the back of the instrument. The operating system
will boot up in less than a minute.
4. Turn off the power switch to shut down the instrument.

Cautions
DO NOT REMOVE COVER
No operator serviceable components inside. Refer servicing to qualified
personnel.
The DS-11 Series is designed for indoor use under the following conditions:Temperature: 15˚ to 35˚ C
Humidity:
35 to 65 %Elevation:
2000m or less
Pollution:
Pollution degree 2
Use only the power supply provided with the instrument. Use of the
instrument in any manner not specified by the manufacturer may impair theprotection provided by the supplied power cord and power supply.

NE PAS OUVRIR L’APPAREIL.
Aucun composant réparable par un utilisateur est inclus. Confiez l'entretien à dupersonnel qualifié .
Le DS- 11 est conçu pour une utilisation en intérieur dans les conditions suivantes :Température : 15° à 35˚C
Humidité: ........35 à 65%
Utilisez uniquement le bloc d'alimentation inclus avec l'instrument. Utiliser l’appareil dansdes conditions non spécifiées par le fabricant peut compromettre la protection offerte
par le cable d’alimentation et le bloc d'alimentation fournis avec l’appareil.

Instrument Rear Panel
The DS-11 Series comes equipped with Wi-Fi, Ethernet and three USB ports. The USB ports
are used to facilitate data transfer to a FAT32 formatted USB storage device and connect
to the accessory FX Module. In addition, the USB ports support the use of select label
printers* and an Opticon OPI 3601 USB barcode reader. USB mouse and keyboard devices
may also be used with the DS-11 Spectrophotometer/Fluorometer.
*

Please refer to our website for a list of supported label printers.
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VCCI (Class B) compliance statement for users in Japan
This is a Class B product based on the standard of the Voluntary Control Council forInterference (VCCI) from Information Technology Equipment. If this is used near a radioor television receiver in a domestic environment, it may cause radio interference. Installand use the equipment according to the instruction manual.
This equipment has been tested for radio frequency emissions and has been verified tomeet CISPR 22.2 Class B.

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3. Instrument Diagram

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4. Software Quick Guides
EasyApps Software Icons
Home

Add

Select All

Overflow
Menu

Edit

ExportPurity Ratio
Alert

Copy

DeleteInformation

Clear
Selected

Progress bars or busy indicators are used to indicate the instrument
is in the process of making a measurement. Please wait until theicon has disappeared before performing additional actions.

The Quick Print icon is only displayed on Report or Graph screens
when a label printer is connected to the instrument.
Auto Export status icons are displayed at the top right of a Run
screen. Ensure Wi-Fi is connected prior to making a measurement.

10Software Buttons
Software Navigation

The absorbance apps Blank button is used to establish areference absorbance within each measurement app. The graphwill not display a spectrum for a Blank measurement.
The absorbance apps Measure button is used for sample
measurements. It is inactive until a Blank measurement iscomplete.
The fluorescence apps Standards Measure button is used tomeasure standards when building a standard curve.
The Samples Measure button is used to quantitate samples.
The fluorescence apps Replicates On/Off button is used to define
if the standards curve enables one or up to three replicates.
The fluorescence apps Basic Measure button is used to makesingle measurements not being read from a standard curve.
Fields with Drop-Down Menus are indicated by black or white
triangles located on the center bottom.
Fields with black underlines are editable by the user. Tapping on
the field will enable a keyboard, a numeric keypad or a dialog box.
Application specific editor options can be accessed using the List
Add/Edit button found to the right of some drop-down menus.
Options buttons are used for such purposes as change units ortrend line analysis parameters in the fluorescence apps.
An accept and return to previous screen button is found in thelower right of some screens. All changes made to a selection are
immediate.

Apps are launched using Home screen icons. Swipe the Home
page to the left for additional icons.
The app Run, Report and Graph screens are accessed either by
the tabs on the top bar or by swiping the screens left or right.
Use the Account Tab drop-down menu on the top action bar in theRun, Report and Graph screens to select a specific account within
an app. Use the Accounts app to create and manage accounts.

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Top Bar Overflow Functions

ScreenCaptureA .png may be exported as described in the chapter entitled"Screen Capture and Export" using this option.

ChangeUnits

Concentration units may be changed in some apps using thisoption.

Clear
SamplesThis function saves and then clears all current sample records
from the Report and Graph screens.

Baseline
Correction

Some apps enable Baseline Correction changes from theOverflow function on the Run screen.

User Guide

The User Guide may be accessed either from the Overflow icon
within any app or by launching the User Guide app.

About

The About feature brings up an information box displaying thecurrent app version number.

Lamp Reset

The Diagnostics app Lamp Reset is used as a means to reoptimize a lamp when necessary.

Tech Support

The Diagnostics app Tech Support feature is used to send
instrument related diagnostics files to DeNovix customer
support.

Exit

Use the Exit function to close an application.

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5. Absorbance Run Screen
Measurement applications generally use a three-page structure consisting of the Run, Reportand Graph screens. The various screens are accessed either by using the top tabs or byswiping the touchscreen left or right.
Activation of 21 CFR Part 11 Compliance Ready Software affects some aspects of the userinterface. Where applicable, additional instructions for 21 CFR Mode operation are provided.
Contact DeNovix or your local Distributor to purchase an activation code.

Run Screen• Blank and Measure: Use the Blank button when blanking with the reference solution
and the Measure button for samples.

• Mode: Use the drop-down to select the measurement mode.
• Sample Name (optional): Tap the input box to display an on-screen keyboard or use an
Opticon OPI 3601 USB scanner to enter sample names.
• Sample Type and Factor Fields: Displays current sample type and associated factors
used for concentration calculations. The fields may be fixed or selectable dependingon the application.
• Absorbance Graph: The spectral plot displays data for the current sample normalized
to a 10 mm pathlength for microvolume measurements. Pinch and zoom anywhere in
the graph to rescale the X or Y-axis.
• Baseline Correction nm: Displayed at bottom of screen. Use the top action bar
Overflow function to modify. Additional baseline correction details are provided withineach relevant measurement app chapter.

Microvolume Measurements
1. Ensure both top and bottom sample surfaces are clean.
2. Pipette 1 μL of the blank solution onto the lower sample surface. Lower the top arm
and tap the Blank button.
3. Remove the solution from both sample surfaces using a clean, dry lab wipe.
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4. Pipette 1 μL of the sample solution onto the lower sample surface.
5. Lower the arm and tap the Measure button. All microvolume measurements arereported in 10 mm equivalent absorbance values.

Cuvette Measurements
Refer to the light path arrow as a guide when inserting a cuvette. Use cuvettes that meetthe following specifications:• Width: 12.5 mm Length: 12.5 mm Height: 45 mm Z height: 8.5 mm• UV wavelength region: Use quartz or UV transparent plastic cuvettes• Visible wavelength region: Use quartz or plastic cuvettes
1. Insert a cuvette pre-filled with the Blank solution. Lower the arm and tap the Blank
button.
2. Insert a cuvette pre-filled with the sample solution. Lower the arm and tap the
Measure button.

AutoRun
1. Perform a Blank as previously described and then select the AutoRun checkbox on
the app Run screen. Pipette 1 μL of the sample solution onto the lower sample
surface.

2. Lower the arm for automatic measurements. Deselect the feature to perform new
Blank measurements. Note: This feature may be used for both microvolume andcuvette mode measurements.

Measurement Modes• Measurement mode selections are made using the drop-down menu found next to the
Measure button on the Run screen. Modes available vary depending on model.
• The Microvolume mode uses 1.0 μL samples pipetted onto the sample surface.

• The microvolume Short Path mode requires 0.5 μL samples pipetted onto the sample
surface. This mode is for high concentration samples and does not use the 0.5 mm
pathlength.
• The microvolume Fast Mode option is primarily for samples in the range measured by
the 0.5 mm pathlength although it may be used for higher concentration samples.

• DS-11+ and DS-11 FX+ include 10, 5, 2, 1, 0.5, 0.2 and 0.125 mm pathlength Cuvettemode options.
• Report screens will include actual absorbance values measured using a specificcuvette pathlength. Graph screens will display all cuvette absorbance values
normalized to a 10 mm value.
14• A new Blank must be made when changing between microvolume and cuvette modes.

21 CFR Mode Measurements• Each blank and sample measurement requires an electronic signature in order to savea result. After each result select to discard or e-sign the result. Procedures are detailed
in the 21 CFR Section of this user guide.
• AutoRun is disabled in 21 CFR Mode.

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6. Absorbance Report and Graph Screens
Report Screen• The Report screen list includes application specific data fields for each sample
measured in the current measurement session.
• Tap rows to highlight and select data for export. The Select All /UnSelect All icons areused to quickly select or deselect all rows.

• The change will be applied to the current Report and Graph screen rows as well as tothe sample information retrieved using the Data app.
• Clear highlighted sample records from the both the Report and Graph screens using
the Delete icon. The data is removed from the current report but is still available using
the Data app.

• Highlighted sample data may be exported or printed using the top action bar Overflow
Screen Capture or Export Selected functions. Additional information is provided in thechapter entitled "Screen Capture and Export".

Graph Screen16• Tap rows to highlight and select / deselect data to display the spectra. The Select All/UnSelect All icons are used to quickly select or deselect all rows.
• Up to 24 samples may be overlaid on the graph. Absorbance apps will display sample
spectra while the fluorescence apps will display the concentration calculated from thestandard curve trend line.
• Color blocks are used as a legend convention.
• Highlight a single row and then tap the Edit icon to add or modify a sample name. Thechange will be applied to the current Report and Graph screen rows as well as to thesample information retrieved using the Data app.
• Clear highlighted sample records from the both the Report and Graph screens using
the Delete icon. The cleared data will be available using the Data app.
• Highlighted sample data may be exported or printed using the top action bar Overflow
Screen Capture or Export Selected functions. The data will be exported as a .csv fileand spectra may be re-graphed using a spreadsheet chart function. Additional
information is provided in the chapter entitled "Screen Capture and Export".

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7. Absorbance Best Practices
Best Practices for Absorbance Measurements• Clean both sample measurement surfaces prior to making the Blank measurement.
• Use dH2O, not detergents or alcohol, for routine sample measurement surface
cleaning.
• Use a dry lab wipe to remove measurement liquids from both the top and bottom
surfaces immediately after each measurement.
• Use 1 μL samples for routine microvolume measurements.
Note: Select the Short Path mode for high concentration 0.5 μL samples.
• Use a fresh aliquot for each measurement.

• Use a fresh tip to deliver each sample aliquot.
• Avoid introducing bubbles when pipetting samples onto the measurement surfaces.
• Ensure sample concentrations fall within absorbance limits of the instrument for
accurate results.
• Use the same buffer a sample is suspended in for the Blank measurements.
• Avoid using buffers such as RIPA buffers that contain components with strong
absorbances at the wavelength of interest.
• Measure a fresh aliquot of the buffer using the Measure button and ensure thespectrum is relatively flat along the baseline before measuring samples.
• For cuvette mode measurements, use cuvettes with 8.5 mm Z heights. Select the
Cuvette option using the drop-down menu next to the Measure button and ensure thecuvette is inserted in the proper orientation.

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8. Tech Team Tips
Initialization• Before the system is powered on, remove all packaging or protective materials frombetween arm and sample surfaces.
• Follow on-screen instructions to clean the sample surfaces.
• Lower the arm and Press OK to complete the system Initialization.
• Although there is no harm in doing so, there is no need to shut down the instrument
each day. The backlight for the screen will automatically turn off to protect the screen
and will switch on when touched.

Connectivity and Results Data
• Use the Settings App to configure Wi-Fi or connect an ethernet cable to the rear
ethernet port on the instrument.
• Within Settings configure email, network printers and network folders.
• Compatible label printer models enable immediate printing of results.
• Use the share icon

to export results to USB or one of the connected methods above.

• All results are saved on the device until deleted. Export during a measurement session
or use the Data App to search for and export results later.
• For ease-of-use, an open access default General account is active when apps are
opened. Use the User Accounts app to set up other accounts, password protect them if
desired and configure app specific launch defaults as desired.

Software Updates• Connect to the Internet and open the Updater App. Check for updates and download
directly to the device. Alternatively, visit our website to download the update package
to a FAT32 formatted USB drive. Insert the USB drive and then launch Updater.

Technical Support• Visit the DeNovix website for instructional videos, Technical Notes and fortroubleshooting tips. Contact your DeNovix Distributor or email info@denovix.com for
help.

19

9. Absorbance Nucleic Acid Apps

dsDNA

RNA

ssDNA

Microarray

The four preconfigured nucleic acid apps are used to quantify nucleic acid samples
based upon absorbance values at 260 nm.

Quick Protocol
1. Launch the appropriate application from the Home screen.
2. Establish a Blank using the appropriate buffer.
3. Enter a sample name.
4. Select a sample type if applicable.
• Enter optional user-defined ng-cm/μL factor (ssDNA and Microarray).
• Select a dye type (Microarray only).
5. Measure a fresh aliquot of sample using the Measure button.
Notes:•

Blank with TE if the sample is dissolved in TE.

•

Ensure that the sample isolation procedure is optimized and that samples are purified
prior to making absorbance measurements.

•

Ensure all solutions are homogenous and well-mixed prior to sampling.

•

Use fresh aliquots for each microvolume measurement.

20

dsDNA, RNA and ssDNA
The basic nucleic acid apps are optimized for the measurement parameters used to
calculate sample concentrations.

Screen Features• Sample Type: The sample type is used to determine which ng-cm/μL factor is used to
calculate the concentration.
• The sample type is fixed for both the dsDNA and RNA apps.
• A Factor Input option along with the default ssDNA sample type is available fromthe selector field for the ssDNA app.
• Factor: The default wavelength-dependent factors used for each app are as follows:
dsDNA: 50 ng-cm/μL RNA: 40 ng-cm/μL
ssDNA: 33 ng-cm/μL• Oligo factors derived from the Calculator app may be copied and pasted directly
into this field.
• Concentration Results: Concentration results are reported in units of ng/μL.
• Units may be changed using the Run screen top action bar Overflow menu. The
units selected at the time of the measurement are saved to the database.
• A260: Reports the baseline-corrected 260 nm absorbance value.
• 260/230: Displays the ratio of the 260 nm and 230 nm absorbance values.

• 260/280: Displays the ratio of the 260 nm and 280 nm absorbance values.
Note: The DNA and RNA apps do not distinguish between the nucleic acid species withina sample. It is important to optimize the isolation protocol to ensure accuratequantitation.

21

Microarray
The Microarray app is used to quantify nucleic acid samples based upon absorbancevalues at 260 nm and dyes based upon dye specific analysis wavelengths.

Screen Features• Sample Type: The sample type selection of ssDNA is the default option for thisapplication. Options include:• ssDNA (Factor = 33 for nucleic acid concentration calculation.)• RNA (Factor = 40 for nucleic acid concentration calculation.)• Factor Input to enable a user-defined nucleic acid factor. Oligo factors derived
from the Calculator app may be copied and pasted directly into this field.
• Dye Type: Cy3 is default selection for this application.
• Nucleic Acid Concentration Results: Results are reported in units of ng/μL.
• Units may be changed using the Run screen top action bar Overflow menu. The
units selected at the time of the measurement are saved to the database.
• Dye/Fluorophore Concentration Results: Results are reported in units of μM.
• A260*: Reports the baseline and dye corrected 260 nm absorbance value. This value
may be lower than the A260 value observed in the absorbance spectra due to thecorrection factors applied.
• AXXX: The baseline-corrected dye specific analysis wavelength absorbance value (e.g
A550 when using the Cy3 dye).

22Dye List
There are 11 preconfigured dye types available for both the Microarray and Labeled
Proteins applications. New dye types may be saved using the List Add/Edit button to theright of the dye list drop-down menu. Refer to the manufacturer of the dye for analysis
nm, extinction coefficient and correction factor information.

Dye

Ext. Coeff

A260 Factor

A280 Factor

Cy3

150000

0.08

0.08

Cy5

250000

0.05

0.05

Cy5.5

2500000.05

0.18

Alexa Fluor 405

34,0000.23

0.7

Alexa Fluor 488

71,0000.3

0.11

Alexa Fluor 555

150,000

0.08

0.08

Alexa Fluor 594

90,0000.43

0.56

Alexa Fluor 647

239,000

0

0.03

Alexa Fluor 680

184,000

0

0.05

Alexa Fluor 700

192,000

0

0.07

Fluorescein/FITC

68000

0.32

0.2

Dyes saved to the list are accessible for both the Microarray and Labeled Proteins apps.
The new dyes may be used by all accounts, including the General Account. The useradded dyes may only be edited or deleted by the account holder or an administrator.
The following information is required in order to save a new dye to the list:• Dye name• Analysis wavelength• Analysis wavelength specific molar absorption coefficient (M -1 cm-1)• 260 nm absorbance correction factor• 280 nm absorbance correction factor
Preconfigured dyes may not be modified or deleted.

23Baseline Correction for Dyes
The software anchors the visual spectrum display to the baseline at 750 nm for all
measurements. It automatically applies a 340 nm bichromatic normalization for the A260
value and uses a sloping baseline between 400 and 750 nm for dye concentration
calculations.
If adding a new dye, it is important to empirically determine if the default 750 nm
selection is appropriate to use as the baseline correction wavelength.
• The baseline correction screen is accessed from the Run screen top action bar
Overflow icon.

• Tap the Add icon to include a user-defined option between 750 and 840 nm.
• The new option will be used for both the visual display and the sloping dye baseline.
• Once a baseline correction nm is selected, it is applied to all subsequent
measurements and is not dye specific. When changing dyes, always confirm that theproper baseline correction is applied.

24

Nucleic Acid Concentration Calculations
A modified Beer-Lambert equation is used to calculate concentrations as follows:c = (A * e)/bc = the nucleic acid concentration in ng/microliter
A = the absorbance in AU
e = the wavelength-dependent factor in ng-cm/microliterb= the pathlength in cm (10 mm)

Baseline Correction
Baseline corrections correct for offsets due to sample particulates. If a baseline
correction is not used, the sample spectrum may be offset from the baseline, resulting ina change in the reported sample concentration. The DS-11 uses an optimized baseline
correction as the default selection. However, the user may elect to define the baseline nm
used for specific measurements.
The baseline correction screen is accessed from the Run screen top action bar Overflow
icon. Once a baseline correction nm is selected, it is applied to all subsequent
measurements within the same measurement session.

Purity Ratios• The generally accepted 260/280 values are ~1.8 for pure DNA and ~2.0 for RNA.
• The 260/230 values for nucleic acids usually range between 1.8 and 2.2.

Troubleshooting Purity Ratios
Issue

Low 260/230

Probable Causes/ Solutions
Dirty measurement surfaces or improper Blank.
Clean the surfaces, measure a new Blank using fresh source of dH20
or sample buffer. Use the same solution (water or buffer) the sample
is in for the blank measurement.
Presence of residual extraction reagent (ex. Carbohydrates, Chaotropic
salts, phenol).
Re-purify the sample, then remeasure. Contact the manufacturer ofthe extraction kit for guidance on how to optimize the procedure.

Dirty measurement surfaces or improper Blank.
High 260/230

Clean the surfaces, measure a new Blank using fresh source of dH20
or sample buffer. Use the same solution (water or buffer) the sample
is in for the blank measurement.

25

Dirty measurement surfaces or improper Blank.
Clean the surfaces, measure a new Blank using fresh source of dH20
or sample buffer. Use the same solution (water or buffer) the sample
is in for the blank measurement.
Low 260/280

Presence of residual extraction reagent (ex. protein, phenol).
Re-purify the sample, then remeasure. Contact the manufacturer ofthe extraction kit for guidance on how to optimize the procedure.

Dirty measurement surfaces or improper Blank.

High 260/230

Clean the surfaces, measure a new Blank using fresh source of dH20
or sample buffer. Use the same solution (water or buffer) the sample
is in for the blank measurement.

Ratio Alerts
The DS-11 Series software displays alert icons within the dsDNA, RNA and ssDNA apps
for samples with purity ratios outside of specified minimum and maximum limits.
Tapping on the icon will pop-up a message with alert-specific information.

The default settings are as follows:
Ratio

Minimum

Maximum

260/2301.8

3260/280

1.65

2.5

Users may elect not to have the alerts show or set custom limits using the Run screen
Overflow menu. The new limits may be used by all accounts, including the General
Account. Saved user-added limits may only be edited or deleted by the account holder oran administrator account holder.
Note: The limits are only enforced for samples above a minimum concentration value. A
blue warning icon will be displayed when the sample concentration is below thethreshold. This warning relates to the validity of ratio measurements at low absorbancereadings, not the accuracy of concentration measurements.

26

10. Absorbance Purified Protein, Peptide Apps

Protein
A280

LabeledProteins

PeptidesQuick Protocol
1. Launch the appropriate application from the Home screen.
2. Establish a Blank using the appropriate buffer.
3. Enter a sample name.

4. Select a sample type.
• New protein or peptide types may be added to the selection list.
• Select a dye type when using the Labeled Proteins app.
5. Measure a fresh aliquot of sample using the Measure button.

Notes:•

If the buffer exhibits significant absorbance at 280 nm, use alternative methods such ascolorimetric assays to quantitate proteins.

•

Ensure all solutions are homogenous and well-mixed prior to sampling.

•

Use fresh aliquots for each microvolume measurement.

27

Protein A280
The Protein A280 application is used to quantify samples based upon absorbance values
at 280 nm.

Screen Features• Sample Type: The sample type and associated mass extinction coefficients options
include:Use the 1A=1mg/ml option when neither the E1% nor Ext Coeff and MW for the purified
protein sample are known.
• Concentration Results: Results are reported in units of mg/mL.
• Units may be changed using the Run screen top action bar Overflow menu. The
units selected at the time of the measurement is what is saved to the database.
• A280: Reports the baseline-corrected 280 nm absorbance value.
• 260/280: Displays the ratio of the 260 and 280 nm absorbance values.

Protein Type List
New Protein types using either user-defined E1% or MW and Ext. Coeff values may besaved using the List Add/Edit button to the right of the sample type drop-down menu.
• The new sample types may be used by any account holder.
• The new sample types may be edited or deleted only by the account holder or an
administrator account.

Sample Type
BSA
1A=1mg/mL
IgG

E1% at 280 nm for 10 mm pathlength
6.67
10
13.7

E1%

User-defined mass extinction coefficient (L gm -1 cm -1) for a 10
mg/mL (1%) solution

MW & Ext Coeff

User-defined MW (Daltons) and molar extinction coefficient(M -1 cm-1)

28

Baseline Correction
Bichromatic normalizations correct for baseline offsets due to sample particulates. If abaseline correction is not used, the sample spectrum may be offset from the baseline,
resulting in a change in the reported sample concentration. The DS-11 uses an optimized
baseline correction as the default selection. However, the user may elect to define thebaseline nm used for specific measurements.
The baseline correction screen is accessed from the Run screen top action bar Overflow
icon. Once a baseline correction nm is selected, it is applied to all subsequent
measurements within the same measurement session.

29

Labeled Proteins
The Labeled Protein application is used to quantify protein samples based uponabsorbance values at 280 nm as well as Dyes and Fluorophores at specific analysis
wavelengths.

Screen Features• Sample Type: The sample type and associated mass extinction coefficients options
include:Sample Type
BSA
1A=1mg/mL
IgG

E1% at 280 nm for 10 mm pathlength
6.67
10
13.7

E1%

User-defined mass extinction coefficient (L gm -1 cm -1) for a 10
mg/mL (1%) solution

MW & Ext Coeff

User-defined MW (Daltons) and molar extinction coefficient(M -1 cm-1)• Dye Type: Cy3 is default selection for this application.
• Protein Concentration Results: Results are reported in units of mg/mL.
• Units may be changed using the Run screen top action bar Overflow menu. The
units selected at the time of the measurement is what is saved to the database.
• Dye/Fluorophore Concentration Results: Results are reported in units of μM.
• A280*: Reports the baseline and dye corrected 280 nm absorbance value. This value
may be lower than the A280 value observed in the absorbance spectra due to thecorrection factors applied.
• AXXX: The baseline-corrected dye specific analysis wavelength absorbance value (e.g
A550 when using the Cy3 dye).

Protein Type List
New Protein types using either user-defined E1% or MW and Ext. Coeff values may besaved using the List Add/Edit button to the right of the sample type drop-down menu.
• The new sample types may be used by any account holder.

• The new sample types may be edited or deleted only by the account holder or an
administrator account.

30

Dye List
There are 11 preconfigured dye types available for both the Microarray and Labeled
Proteins applications. Refer to the "Microarray" section of the chapter entitled "Nucleic
Acids" for more information.

Baseline Correction
The software anchors the visual spectrum display to the baseline at 750 nm for all
measurements. It automatically applies a 340 nm bichromatic normalization for the A280
value and uses a sloping baseline between 400 and 750 nm for dye concentration
calculations.
If adding a new dye, it is important to empirically determine if the default 750 nm
selection is appropriate to use as the baseline correction wavelength.
• The baseline correction screen is accessed from the Overflow icon.

• Tap the Add icon to include a user-defined option between 750 and 840 nm.
• The new option will be used for both the visual display and the sloping dye baseline.
• Once a baseline correction nm is selected, it is applied to all subsequent
measurements and is not dye specific. When changing dyes, always confirm that theproper baseline correction is applied.

PeptidesThe Peptide app is used for low concentration samples which do not have aromatic
residues such as Trp, Tyr or Cys-Cys disulphide bonds. The Protein A280 app is
recommended when the sample does contain aromatic rings.

Screen Features• Sample Type: The first two sample types included in the sample type drop-down arepreconfigured for both the analysis wavelength and the corresponding E 0.1%.
• Sample type and associated E 0.1% coefficients options include:
Sample Typee215 nme205 nmE0.1%

E 0.1% at specified nm for 10 mm pathlength

Analysis Wavelength

11.7

215 nm(recommended)

31

205 nmUser-defined mass extinction coefficient(L gm -1 cm -1) for a 1 mg/mL (0.1%)
solution

215 or 205 nm
User Option• Analysis Wavelength Selector: The radio button selector will appear for all sample
types except the preconfigured e215 nm and e205 nm options. Note: Extinction
coefficients are wavelength dependent.
31• Concentration Results: Results are reported in units of mg/mL.
• Units may be changed using the Run screen Overflow menu. The units selected at
the time of the measurement is what is saved to the database.
• AXXX: Reports the baseline-corrected analysis wavelength absorbance values (e.g
A205 or A215).

Protein and Peptide Concentration Calculations
The Beer-Lambert equation is used to calculate concentrations as follows:
A = E1% * b * c
c = the protein concentration in g/100 mL
A = the absorbance in 10 mm equivalent
E1%= the percent extinction coefficient (L gm -1 cm -1) for a 10 mg/mL (1%) solutionb= the pathlength in cm (10 mm)
The following equation is used to convert g/100 mL to mg/mL concentrations:c (mg/mL)= (A/E1%) *10
The relationship between percent extinction coefficient (E1%) and molar extinction
coefficient (Ext. Coeff) is:
E1% = (Ext. Coeff *10) / molecular weight of protein (Daltons)
Note: The Peptide app uses E 0.1% values whereas the Protein A280 app uses E 1%
values.

The DeNovix software reports concentrations in mg/mL units for the Protein A280,
Labeled Protein and Peptide applications. The concentration is determined based upon
the absorbance value at the analysis wavelength used for the measurement.

32

Ratio Alerts
The DS-11 Series software displays alert icons within the Protein A280 for samples with
A260/280 purity ratios outside of specified maximum limits. Tapping on the icon will
pop-up a message with error specific information.
In general, pure protein samples will have a ratio below 0.57. The default software valuethat will trigger an alert is 0.7.
Users may elect not to have the alerts show or set custom limits using the Run screen
Overflow menu. The new limits may be used by all accounts, including the General
Account. Saved user-added limits may only be edited or deleted by the account holder oran administrator account holder.
Note: The limit is only enforced for samples above a minimum concentration value. A
blue warning icon will be displayed when the sample concentration is below thethreshold. This warning relates to the validity of ratio measurements at low absorbancereadings, not the accuracy of concentration measurements.

33

11. Absorbance Colorimetrics App
Refer to the manufacturer of the assay reagent for assay specific instructions.

BCA

Bradford

Lowry

Pierce 660

Quick Protocol
1. Launch the app from the Home screen.
2. Select the assay type on Run screen. Navigate to the Standard Curve screen.
3. Select the appropriate microvolume or cuvette mode prior to making the Blank
measurement.

4. Establish a Blank using the appropriate buffer or the 0.00 mg/mL standard.
5. Generate a new Standard Curve by measuring at least one replicate for a minimum of
2 standard concentrations. Alternatively, apply a previously saved curve selectedfrom the drop-down menu.

6. Navigate to the Run screen.
• Optional: Enter a sample name and dilution factor to be applied to the reported
concentration.
7. Quantitate the sample using the Measure button.
8. Notes:•

The Graph Flip button is available on the Run and Graph Screens in the Colorimetrics andCustom Standard Curve apps. The flip option is not available when reviewing the resultsin the Data app. Only the absorbance style graphs will be displayed.

•Standard Concentrations: Minimum 2, Maximum 8.

Generating a Standard Curve
1. Use the drop-down menu on the Std Curve screen to select New Curve or to import a
saved standard curve or standard curve concentration list.
2. If the New Curve option is selected, tap the Enter Standards button to enable a popup box to enter a list of standard concentrations for the current measurement
session.
• The table enables up to 7 standard concentrations in addition to the predefined
0.00.
• The 0.00 concentration is used for the diluent (no analyte) plus the assay reagent.
Although not recommended, the 0.00 concentration may be edited.
3. Measure at least one replicate of each standard concentration by highlighting thestandard concentration row and then tapping the Measure button.
34• Up to 5 replicates may be measured for each concentration. Use fresh aliquots foreach measurement when using the microvolume mode.
• The software will advance after each measurement until the fifth replicate has
been measured. If additional measurements are made, the fifth position will beoverwritten.
• A minimum of two standards must be measured before the Measure button is
active on the Run screen.
• Select a standard row or individual replicate then tap the Delete icon to display adrop-down list of delete options.
• Use the Undo icon to restore the most recent edit or delete action.

35

Line Fit
The average of the replicates is used to determine a best-fit trend line of the data set. The
trend line equation is applied to the sample absorbance values to calculate
concentrations.

Options include:• Linear• 2nd Order• Interpolation: This option draws a straight line between each point.
Note: The software will extrapolate concentrations for samples with absorbances 15%
above the absorbance values associated with the highest standard for linear fits only.

Saving a Standard Curve
A standard curve or a series of standard concentrations may be saved and reused at alater date.

• Use the List Add/Edit button to the right of the curve list drop-down menu to save acurve or concentration list.

Editing a Standard Curve• The curve is in an editable state when the Lock icon is unlocked.
• When a previously saved curve or concentration list is imported, a red Lock icon willappear. Tap the icon to unlock the curve data set to enable modifications and newabsorbance measurements.

• All modifications to a curve (new or saved) are effective immediately. It is important tosave a curve with a new name prior to making any changes if you do not want tomodify the original curve.
• The only way to recall absorbance data for a standard curve is to save the results as asaved curve before exiting the app.
36• Although all accounts may use any previously saved standard curve or saved
concentration list, only the curve account holder or an administrator may modify ordelete a saved curve or concentration list.

Exporting a Standard Curve
The standard curve replicate values may be exported using the Screen Capture function
described in the chapter entitled "Screen Capture and Export."
Note: The standard curve data is not available in a .csv format. Use the Screen Capture
function to export a .jpg showing the curve replicate values.

37

BCA
The bicinchoninic acid assay (BCA assay) is used to quantify protein by measuring the
Cu-BCA chelate formed in the presence of protein.
• The reaction product is measured at 562 nm using a baseline correction at 750 nm.

Bradford
The Bradford assay is based upon a protein-induced absorbance shift of a Coomassie
Blue dye as a method to determine protein concentration.
• The reaction product is measured at 595 nm using a baseline correction at 750 nm.
Note: Some Bradford formulations may form particulates during prolonged
incubations. It is recommended that the cuvette option be used when using these typesof formulations. The particulates may interfere with the shorter pathlengths used forthe microvolume measurements.

Lowry
The modified Lowry assay is used to quantify proteins based upon the absorbance oftetradentate copper-protein complexes.
• The reaction product is measured at 650 nm using a baseline correction at 405 nm.

Pierce 660
The Pierce 660 nm Protein Assay is used to measure a reddish-brown dye-metal complex
that changes to green upon protein binding.
• The reaction product is measured at 660 nm using a baseline correction at 750 nm.

3812. Absorbance UV-Vis App

UV-VisThe UV-Vis app is used to monitor up to 6 specific analysis wavelengths. Absorbancevalues for all wavelengths from the user selected wavelength ranges are saved for eachmeasurement and can be exported as a .csv file using the Export function from theReport or Graph screens.

Quick Protocol
1. Launch the UV-Vis application from the Home screen.
2. Establish a Blank using the appropriate buffer.
3. Enter the analysis nm in the first input field. This wavelength is used to determine
which pathlength is utilized by the SmartPath technology for microvolume
measurements. Enter up to five additional wavelengths of interest.

4. Enter a sample name.
5. Measure a fresh aliquot of sample using the Measure button.

Wavelength List
A list of between 1 to 6 wavelengths may be saved and recalled by using the Overflow
icon to the right of the wavelength list drop-down menu.

Wavelength Range Selection
There are two wavelength ranges available for the UV-Vis app. Use the checkbox feature
to select between the 220 to 750 nm or the 190 to 840 nm options. Changing ranges willautomatically save and then clear current results. A new Blank is required when switchingranges.
Use the Custom Formula App to create a method that utilizes a user-defined wavelength
range.

Cursor Position
The UV-Vis app Run Screen graph includes a moveable cursor initially set at the analysis
wavelength. Moving the cursor allows the user to find the absorbance value of any
wavelength after a measurement is made.
Note: The cursor wavelength absorbance value is a temporary value not saved by thesoftware.

39Baseline Correction
The baseline correction normalizes the entire spectrum using the absorbance value ofthe wavelength specified and corrects for baseline offsets due to sample particulates.
The default selection is set to 750 nm for the UV-Vis app.

If a baseline correction is not used, the sample spectrum may be offset from thebaseline, resulting in a change in the reported sample concentration.
The baseline correction list is accessed from the Overflow icon. Once a baseline
correction nm is selected, it is applied to all subsequent measurements within the samemeasurement session.

40

13. Absorbance OD 600 App

OD 600This application is generally used to determine the optical density of microbial cell
cultures at 600 nm. Conversions to cells per mL are based upon a user-defined factor.

Quick Protocol
1. Launch the app from the Home screen.
2. Establish a Blank using the appropriate buffer.
3. Enter a sample name.
4. Enter a cell conversion factor (optional).
5. Measure a fresh aliquot of sample using the Measure button.
Notes:•All cell type specific conversion factors are user derived.

•

Ensure culture is well mixed prior to sampling.

•

Use fresh 1 µL aliquots for each microvolume measurement.

•

Although microvolume OD 600 measurements can be made, the cuvette 10 mm mode isrecommended for this app. This option is available on the DS-11+ and DS-11 FX +.

41

Unique Features• A600: The OD 600 is a measure of the light scattered by the cell suspension solution.
Reported values may differ for the same sample measured on different
spectrophotometer systems as values are dependent on both the cell type and theoptical configuration of the spectrophotometer.
o

It is recommended that an optimal harvest density and the linear range of
growth curves be empirically determined for each microbial cell type whenusing a new spectrophotometer.

• Cell Number Conversion Factor: The cell number conversion factor is used to convert
the 600 nm value into the number of cells per mL for the sample by multiplying theabsorbance value by the factor. Cell numbers are reported in terms of 1 * 108 cells. The
factor must be entered into the appropriate field prior to a measurement.
Note: The cuvette mode selection (i.e the path length) must be taken into accountwhen determining target OD 600 values or entering cell conversion factors. Whenmaking microvolume measurements, the OD 600 values reported and used for cellnumber calculations are 10 mm equivalent values.

Baseline Correction
As microbial cell culture OD 600 values are measurements of light scattering, the DS-11
software does not use a bichromatic baseline normalization unless specified as a user
selection.
The baseline correction screen is accessed from the Overflow icon. Once a baseline
correction nm is selected, it is applied to all subsequent measurements within the samemeasurement session.

42

14. Absorbance Kinetics App

Kinetics

The Kinetics application is a cuvette mode only application available for the DS-11+ and
DS-11 FX+ models.

Quick Protocol
1.

Launch the app from the Home screen.

2.

Use the Create Method button on the Run screen to define the parameters of themethod.
• The button will change to a drop-down menu after at least one method has been
defined. Use the List Add/Edit button to the right of the drop-down to define
additional new methods or edit previously saved methods.

3.

Navigate to the Run screen and tap the Heater button to preheat the cuvette block tothe selected temperature.

4.

When the Heater temperature field displays the set temperature, insert the cuvetteand establish a Blank using the appropriate buffer.

5.

Insert the cuvette with the sample solution and tap the Measure button.
Notes:•

Use cuvettes with Z heights of 8.5 mm. Use the light path arrow as a guide wheninserting a cuvette into the cuvette block.

•Use a quartz or UV transparent plastic cuvette when using methods that include the UV
wavelength range.

Define Method Screen Features• Method Name: A unique name is required for each method.
• Analysis nm: Enter the primary wavelength of interest for the method. The absorbancevalue at this wavelength will be plotted versus time on the Trend plot.
• Analysis nm 2: Optional 2nd wavelength of interest for the method. The absorbancevalue at this wavelength will be plotted versus time on the Trend plot.
• Wavelength Range: Define a range between 190 to 840 nm.
• Baseline Correction Wavelength: 750 nm is the general recommendation, but the
optimal wavelength should be empirically determined.
• Heater Set Point: The heater may be set to temperatures between 37ºC to 45ºC.

43Stage Selections
Up to three stages of timed intervals may be included for each method. The parameters
for each stage include:• Delay: This is the time before the first measurement of each stage.
• Interval: This is the time between measurements. The minimum interval is 5 seconds.
• Duration: This is the cumulative time of the individual stage not including the delay. A
duration will be rounded down to the nearest even multiple of the interval.
Example: Interval = 10 seconds, Duration = 31 seconds
Duration rounded down to 30 seconds.

44

Run Screen Features• Method: Select the method of choice using the drop-down menu. Use the List Add/Edit
button to the right of the drop-down to create or edit methods. All methods areavailable to all accounts however, only the account holder or an administrator may edit
or delete a method.
• Graph Type Flip Button: Graph types may be switched during the run.
• Spectra: Absorbance vs wavelength• Trend: Absorbance vs elapsed time for analysis wavelength(s)• Heater Control: Tap the On/Off button to control the heater. The heater may overshootthe method set point before reaching a equilibrium + 0.5ºC of the set point.
• Timer: This feature is used to monitor the sample solution warm-up time. The timer isused in a count-up only mode but is not used to track the measurement time.

• Stop Button: A Stop button replaces the Measure button on the Run screen during theKinetics run. Tapping this button will end the measurement and save all data
accumulated up to that point. The Measure button will be available when the run isfinished.
• Results Table: A scrollable table with the absorbance values at the specified
wavelength(s) per time is displayed on the Run screen.

Heater Temperature• The temperature display box is color-coded for quick reference:• White: Heater is off.

• Yellow: Heater is on, heater is not at method set point.
• Orange: Heater is on, cuvette holder block has reached the method set point within+ 0.5ºC.

Sample Solution Temperature• The solution in the cuvette may not reach the set point as quickly as the heater. Use
the Run screen timer as a means of monitoring the elapsed warm-up time. Below are
estimated warm-up times.
The times were determined after a 10 mm plastic disposable cuvette filled with water wasinserted into the cuvette block already heated to the method set point. Actual times may varyand should be empirically determined for each assay protocol.

• The temperature display box does not measure the temperature of the solution in the
cuvette.

Solution Start Temp

4ºC

Room Temperature

Heater Set Point Temp

37ºC

45ºC

37ºC

45ºC

Warm-up Time (mins)

15 to 20

15 to 20

10 to15

10 to 1545

Report, Graph, Trend Screens• Report Screen: Unlike other DS-11 measurement apps, the results displayed in the
Kinetics Report screen list are associated with one assay run. Each time a new assay
run is initiated, the previous results will be saved and then cleared from the Report,
Graph and Trend screens. The cleared data may be accessed using the Data app.
Note: It is normal for the software to experience minor delays in reporting kinetics data
information relative to the actual measurement time point. The actual time eachmeasurement is initiated is what is reported in the Elapsed Time field.
• Graph Screen: Displays the absorbance for the method-defined wavelength range foreach time point.
• Trend Screen: Displays the absorbance vs. elapsed time for method-defined analysis
wavelength(s). Use the action bar timers to narrow the time points for export or screen
capture.

46

15. Absorbance Custom Methods Apps

Std Curve Methods

Formula Methods

These applications are used to create, save and access user-defined methods.

Quick Protocol
1.

Launch the applicable Custom Methods app from the Home screen.

2.

Use the Create Method button on the Run screen to define the parameters of themethod.
• The button will change to a drop-down menu after at least one method has been
defined.
• Use the List Add/Edit button to the right of the drop-down to define additional new
methods or edit previously saved methods.
• All methods are available to all accounts however, only the account holder or an
administrator may edit or delete a method.

3.

Establish a Blank using the appropriate buffer. If the method is a standard curve type,establish the Blank and measure the standards from the Std Curve screen before
navigating to the Run screen.

4.

Enter a sample name (optional).

5.

Measure a fresh aliquot of sample using the Measure button.

47

Primary Settings
Each new method requires a unique name. In addition, the following parameters must be
defined:• Analysis nm: Enter the primary wavelength of interest for the method.

• Absorbance values at the analysis nm will be used to generate a curve forStandard Curve methods. The analysis nm will be also be used to determine whichpathlength is utilized by the SmartPath technology for microvolume
measurements.

• Baseline nm: A baseline correction wavelength is required for the Standard Curvemethods but not for the Formula Methods. Bichromatic normalizations correct forbaseline offsets due to sample particulates. If a baseline correction is not used, thesample spectrum may be offset from the baseline.

• Although the general recommendation would be to use 340 nm for UV only

wavelength ranges and 750 nm for full range methods, the optimal baseline
correction wavelength should be empirically determined.

• Wavelength Range: The software will perform a wavelength optimization function
each time the wavelength range is defined or edited within a method.

Custom Standard Curve Methods
In addition to the primary settings described above, the Standard Curve app also requiresthat a units label be defined.

• Once a new method is established or a previously saved method is selected, navigate
to the Std Curves screen and follow the steps outlined for Generating a Standard Curvein the chapter entitled "Colorimetrics".
• Standard Curve methods function the same way as preconfigured Colorimetrics apps.

48

Custom Formula Methods
In addition to the primary analysis wavelength, the Formula Methods app enables theuser to include up to four additional results for each measurement. The result fields may
be used to monitor additional specific wavelengths or have the software perform routine
calculations based upon absorbance values measured at specific wavelengths.
• Result Name: Enter a name for each custom formula.
• Custom Formulas: Tap on the custom formulas input field to display a pop-up dialog.
The following functions are available:• Advanced: When checked, this feature allows the user to designate that the method
uses a Savitzky–Golay filter instead of the default boxcar method to smooth data.

Function

Description

Numerical Operations

+ add

A(x)

Absorbance at wavelength x

Log(x)

Log of xln(x)Natural Log of x^

Exponent
Example 4^3 equals 4x4X4√Square Roote

Scientific notation
Example 2e3 equals 2 x 103 or 2000

V1, V2- subtract * multiply

÷ divide

Variables that are entered on the Run screen
prior to each measurement.

49Formula Guidelines• Use the A(x) button on the input screen to use the absorbance value result of a specificwavelength in the formula. Enter the wavelength within the parenthesis.
Example: A(260)• Check that closed sets of parentheses are included when entering complex formulas.
Example: Log(A(260)) is correct. Log(A(260) is incomplete.

• Do not enter an equal sign before the equation. This is implied within the software.
Example: A(260)/A(280) is correct while = A(260)/A(280) is incorrect.

• The software automatically applies the baseline correction specified in the method
set-up. Do not include baseline corrections in user-defined equations.

• 10 mm pathlength equivalent absorbance values are used and reported for
microvolume measurements.

Cuvette IQOQ mode
• The cuvette IQOQ 10 mm option is exclusively for use with the Formula Methods app
when running the DeNovix suggested IQOQ procedure. Contact customer support for
more information.

50

16. Fluorescence: Basic Operation
DeNovix Spectrophotometer/Fluorometer software includes both absorbance andfluorescence apps. The fluorescence app icons will appear on the first page of the Home
screen for the DS-11 FX and DS-11 FX+ models. The inactive versions of the icons willappear on the second page for DS11 or DS-11+ units when a FX Module USB accessory is
not detected.
Activation of 21 CFR Part 11 Compliance Ready Software affects some aspects of theuser interface. Where applicable additional instructions for 21 CFR Mode operation areprovided. Contact DeNovix or your local Distributor to purchase an activation code.

The table below lists the four LEDs included in all FX models. Users must select theappropriate LED for the assay that they choose for quantification.

LEDs

Excitation Filter Range

Emission Filter Range

UV361 - 389 nm

435 - 485 nm

Blue

442 - 497 nm

514 - 567 nm

Green490 - 558 nm

565 - 650 nm

Red

613 - 662 nm

664 - 740 nm

Fluorescence Measurements
1. If using the FX Module accessory, connect the module to the DS-11/DS-11+ using
one of the three USB ports.
2. Insert a PCR tube pre-filled with the fluorescent solution. Close the cover and tap
Measure.
Notes:•

Use clear thin-walled 0.5 mL plastic PCR tubes only•

Measure 200 µl volume samples.

Best Practices• Ensure all sample concentrations in the thin-walled assay tubes fall within the limits of
the assay or reagent kit for accurate results.

• Use 200 μL volumes in a clear thin-walled PCR tube.
• Lower the cover before tapping the measure button.
• Avoid introducing air bubbles into the sample solution when mixing samples.
• Follow assay reagent manufacturers' recommendations regarding temperature,incubation time, and protection from ambient light.
51

• Follow assay reagent manufacturers' recommendations regarding suggested standard
curve concentrations and data analysis.
• Ensure all samples and standards are treated identically in terms of incubation times
and temperature.

• Minimize assay tube and solution temperature fluctuations as these may impact theaccuracy of the assay. Samples at higher temperatures will generally have lower
fluorescence.
• Do not label the side of an assay tube as this could interfere with the sample
measurement.

52

17. Fluorescence: Standard Curve Method Apps
The EasyApps listed below are designed using the same basic architecture. Each app
includes a choice of four excitation LEDs (UV, Blue, Red, Green) and a variety of assays.
The end user is responsible for selecting the proper choice based on the analyte that will
be used for quantification.
•DeNovix dsDNA Broad Range•DeNovix dsDNA High Sensitivity

FluorodsDNA•DeNovix dsDNA Ultra High Sensitivity•Quant-iT PicoGreen•Quant-iT•Quant-iT

dsDNA HS
dsDNA BR

•DeNovix RNA Assay

FluoroRNA

FluorossDNA

FluoroProtein•Quant-iT

RiboGreen•Quant-iT RNA HS•Quant-iT RNA BR•Qubit RNA HS•QubitdsDNA BR
dsDNA HS
•Quantifluor dsDNA•Quantifluor One dsDNA•Qubit 1X dsDNA HS•Qubit 1X dsDNA BR•Qubit•QubitRNA BR•Quantifluor RNA•Quant-iT microRNA•QubitmicroRNA•Quant-iT

OliGreen
ssDNA•Quantifluor ssDNA•Qubit•Quant-iT

Protein•Qubit Protein•Qubit Protein BR

Fluoro•All entries to be defined by the user
Std Assays

Quick Protocol
1. Launch the app from the Home screen.
2. Select an excitation LED using the drop-down menu on the Run screen.

3. Generate a new curve:•

Insert the standard (200 μL total assay volume in a thin-walled PCR tube) into thesample holder and lower the cover. Measure at least one replicate for a minimumof 2 standard concentrations.
53

•

Alternatively, import a saved curve or list of sample concentrations

4. Tap the Samples radio button.
• Optional: Enter a sample name and dilution factor to be applied to the reported
concentration.
5. Quantitate a sample using the Measure button.

Refer to the manufacturer of the assay reagent for assay specific instructions.

Note: DeNovix and QubitTM assays will have predefined standard concentrations and specified units.

54

Run Screen- Assay and Curve Selections

Excitation Source (LED) and Assay Selection• Select the LED from the drop-down menu in the left panel. The user must choose theappropriate LED for the analyte in use.
• New assays may be entered using the List Add/Edit button.
• User defined assays may be used by all accounts but may be modified or deleted onlyby the account owner.

Curve Options
Generate New Curve• Choosing this option will pop-up a dialog window used to enter the concentration
values for the standards.
• Verify the concentrations of the standards for the LED / Assay chosen. The standard
concentrations for all other assays are determined by the user at the time of the assay.
• Trend line analysis options and concentration units used may be changed using theadvanced options button.
• Blank: If selected, the first row in the standards table is used to measure a Blank.
The average RFU value of the blank measurements will be subtracted from all
standard and sample measurements. If the Blank is not selected, the initialconcentration for preconfigured assays will be set to 0.00. This standard istypically the reagent/fluorophore solution without any nucleic acid or protein.

• Trend Line: If selected, the trend line will be forced through the lowest standard
concentration. When a Blank is used, the trend line will be forced through the graphorigin (0,0).

55

Use Previous Curve or Std Values• Choosing this option will pop-up a dialog window with a radio button selector for saved
standard curves and saved standard curve concentration lists.
• All modifications to a curve or list are effective immediately. It is important to save theselection with a new name prior to making any changes if you do not want to modify
the original curve or standards list. Changes to a curve do not affect previously
measured samples.
• Although all saved lists and saved curves are available for use by all accounts, only theaccount holder may modify the selection.

Run Screen- Standard Curve View

• The Stds button will pop-up the Edit Concentrations for Standard Curve window.
• The Delete and Undo icons are used to manage the RFU values within the table.
• The Save button will pop-up the Save Values window. Either concentration values orconcentration values with the associated RFU values may be saved.
• The New Curve button is used to generate a new curve or load a previously saved
curve. All sample data generated using the Samples radio button will be automaticallysaved and accessible using the Data app.
• The Replicates arrow button enables the use of up to three replicate measurements
per standard concentration. The average of the replicates will be used to generate thetrend line.

56

Run Screen- Sample Results View

• Use the Samples radio button to display the measurement results view.

• The samples Measure button will be disabled until one replicate of at least two
standards are measured using the standard curve view.
• The Concentration from Curve results are calculated directly from the standard curve
trend line. Results are reported in terms of the units used to derive the trend line.

• The Optional Dilution Factor (or the µL Added value for Qubit assays) will be applied
as a multiplier to the Concentration from Curve value and the result reported in the
Sample Stock Concentration field.
• The Sample Stock Concentration results are reported in terms of the units selected by
the user. The value saved in Report will be displayed in terms of the units in use at thetime of the measurement.

New Standard Curve Assays/Methods
Each new method requires a unique name. In addition, the following parameters must be
defined:Excitation Source• Use LED Radio buttons to select the excitation source.
• The LED Wizard may be used to determine a compatible excitation source if not
known. The software will make a measurement using each of the four excitation
sources and will report the associated RFU in the color-coded boxes.
• Some fluorophores do not exhibit significant fluorescence unless bound to aprotein or nucleic acid. It may be necessary to set up an assay reaction to best use
the LED Wizard.
57• The standard curve assay methods use one excitation source to determine theconcentration of a sample based upon the RFU measured using the corresponding
emission filter set.
Advanced Options• Use the Advanced Option buttons to set both the Trend Line/Blank selections aswell as the standard curve units.
Although all accounts may use any saved method, only the method account holder or an
administrator may modify or delete the new method.

58

18. Basic Fluorometer App
Basic Fluorometer

This app enables DeNovix systems to be used as a versatile fluorometer for applications
such as dye QC checks and assay development. The app is especially useful for
fluorophores with significant Stoke shifts as it allows the user to excite a sample with
one LED and obtain RFU results from multiple emission channels.

Quick Protocol
1. Launch the app from the Home screen.
2. Select an excitation LED using the radio buttons.
3. Optional: Create and Save a used defined method (LED selection and user defined
assay name).
4. Optional: Enter a sample name.

5. Tap the Measure button.

Excitation Selection and Emission Results• Select an excitation source (LED) or LED plus fluorophore combination.
• The selected LED is the only excitation source used during a measurement. However,
the emission RFU will be collected for each longer wavelength emission filter set.
• For example, if the blue LED is selected, the emission results for the blue, green
and red channels will be reported. If the green LED is selected, only the green andred channel results will be reported.
• User defined fluorophores may be entered using the List Add/Edit button.
59• The Add button will pop-up a window that includes a LED Wizard. Tapping the
Wizard button will result in the sample being excited by each LED and the RFU
measured by the corresponding detector. The user can select the LED mostcompatible with the method.

60

19. Data Export and Print Options
Export Options
From the Report or Graph screen, sample data may be exported via email, to network
printers, label printers, network folders or saved to a FAT32 formatted USB flash drive.
Export options vary depending on the destination. For instance, the full contents of a csv
file cannot be sent to a network printer.

Export Formats
CSV file• The default .csv file format for each absorbance measurement app includes all
absorbance vs wavelength data for the app specific measurement wavelength range
as well as the calculated data displayed on the app Report screen. The csv file can besaved to USB, saved to a network folder or emailed.
• To open an exported .csv file on a computer, the DeNovix instrument and the computer
must both be set to use either period or comma number formats. The instrument’s
number format is determined by the language selected in the Settings app.
PDF Report• A pdf report file can be generated for each measurement app. The pdf can be saved toUSB, emailed, printed to a network printer or saved to a network folder.

Screenshots• Use the overflow menu to capture the active screen. This is a convenient way to export
spectral graphs from the Graphs page.
• The png file may be exported by email, saved to a network folder, saved to a USB driveor printed to a network printer.

Export Via Email• Screen captures, .csv files and pdf summary reports may be exported via email.
• Use the User Accounts app Address Book to save frequently used email addresses.
• It is recommended that a new, dedicated POP3 Gmail or Outlook account be used forall outgoing email from the DS-11. This type of account works very well with the
instrument's operating system and prevents personal incoming email from being
stored on the unit.

61

Export to a Network Folder
The instrument can export to SMB network folders connected to the same network as the
instrument. For best results connect to the network through an ethernet connection,
especially if exporting pdfs and images. See Settings for more information.

USB• Screen captures, pdf reports and data .csv files may be saved to a FAT32 formatted
USB flash drive.
• There are two USB ports on the back of the instrument and one on the side although
only one storage device is recognized at a time. The two additional ports may be used
for the FX Module accessory, label printers, keyboards, mouse and barcode readers.
• DO NOT USE INSTRUMENT USB PORTS TO CHARGE OTHER DEVICES.
• DO NOT CONNECT MOBILE PHONES TO USB PORTS.

Print Options• The DS-11 can print to networked printers or to select label printers. All label print-outs
are in black and white. See our website for a list of supported label printers andsupported label sizes.

Network Printers• Screenshots and pdf summary reports may be printed to network printers.
• Use the Settings app to search for and add printers. Printers that are configured as
driverless CUPS printing are supported.
• Please contact DeNovix or your local distributor for a list of recommended printers if
your current printer is not recognized on the network.

6220. Utility Apps and Functions

User
Accounts

Data

Settings

UpdaterStandard Mode Instructions
This section describes functionality for instruments that are not running in 21 CFR Mode.
Please see the 21 CFR Utility Apps and Functions section for details about how the apps
are configured in that mode.

User Accounts App
The User Accounts app allows users to create and manage individual accounts. Users
can adjust their default settings. Accounts are also used as a means of segregating datawhen performing searches in the Data app.

App Structure
Accounts are listed in the left pane of the screen. A menu of app function options ispresented in the action bar, where the selected option is highlighted with a blue
background.
Select a user account from the dropdown list in the top grey bar and select an option to
edit: Profile, Report Emails, File Share, and Defaults.

App Functions
The basic functions controlled using the Account app are as follows:•

Adding and deleting accounts•

Managing passwords for accounts•

Managing email addresses associated with an account•

Setting account specific app protocol preferences

Default System Accounts
There are two preconfigured system accounts built into the software - the General
Account and the Primary Administrator Account. These accounts may not be deleted.

Primary Administrator•

This account is used to manage instrument settings. It is not used within themeasurement applications.

•

The primary administrator account is not initially password protected. A password
may be applied at any time.
63

General Account•This account is used as the default selection for all apps each time an app is opened.
This account may not be password protected or deleted.

User Account Types
There are two types of accounts that may be added, edited or deleted.
User Added Standard Accounts
Any user may add a standard level account. It is not necessary to select an accountbefore adding a new standard account.
Standard accounts may only modify or delete protocols or emails created from within
their account.

User Added Administrator Accounts•

An administrator level account may only be created by another administrator. The
primary administrator or another existing administrator account must be highlighted
in order to enable the adding of a new administrator.

•

Administrator accounts may modify or delete user entries of any sort created fromwithin any account. A drop-down menu is used to select the desired account.

•

Administrators may change the password for any account as well as delete any
account.

Account Passwords•

Passwords are optional for all added administrator or standard user accounts.

•

Contact the holder of an administrator account if a standard user account password
is forgotten.

•

Contact DeNovix customer support or your local distributor if the Primary
Administrator password is forgotten. Please have the serial number of the
instrument available when requesting help for the Primary Administrator password
reset.

Deleting an Account•When an account is deleted, all protocols and custom report formats created by that
account are reassigned to the General Account.

•

The account specific saved data will also be permanently removed from the
instrument at the time the account is deleted.

Tab - Email Addresses
Multiple “to” email addresses for exporting results may be set up for each account. The
nickname is used in the drop-down list presented on an export destination dialog box.
64

Tab - Defaults
Some application specific default settings may be defined on a per account basis.
Launch the Accounts app from the Home screen and then use the drop-down menus toselect the account, the app and the setting of interest.
Note: The default selections for the General Account may not be modified.

Data App
This app allows the user to search for past data by user account, date or application.
Data can then be added to the Report and Graph screens for review and export. Previous
results can be deleted from within the Data app.

Search Options• Data is automatically filtered based upon the Account selected using the tab on the top
action bar.
• Once the filter criteria have been selected, tap the Search button at the bottom of thescreen. Tap any column header to sort the results list.
• Highlight the sample(s) of interest and tap the Add to Report button to include thesamples on the Report and Graph screens. Blank measurements may be included in
the list but will not provide any absorbance data.
• Data from the same app type for the samples to be added to the Report or Graph
screens. Clear the previous selects to find data from a different application.
• Note: The Data app does not include a Graph screen for fluorescence apps.

Exporting and Deleting Data
• All data is automatically saved to the DS-11 onboard computer database at the time of
measurement.
• The Export Selected Samples function available from the Report and Graph screen are
the same options available in the Report and Graphs screens discussed in the previous
Data Export and Print options section.
• When the export function is used, the data is not deleted from the database andcan be accessed using the Data app.
• Only one Kinetics run at a time may be added to a Report for export from the Data
app.
• The Delete function available from the Report and Graph screen in the Data app.
• When the Delete function is used, the data is permanently deleted from the instrument
database and cannot be restored to the instrument.
65• The storage capability of the DS-11 Series is sufficient for several years of data for alab with average use.

Settings App
The Settings app allows General accounts to see basic system information.
Administrator accounts can access the Permissions tab to adjust access to systemsettings. The Settings app provides access to the following functions and information:

System Info
View software and firmware versions, IP addresses, current language and hostname.
Date/Time
Select manual or automatic date and time options.
Language
Select the language of operation for the device. Not all languages are fully translated.
Setting the language also determines whether a period or a comma is used for thedecimal place.

Network Information
The Wi-Fi and Ethernet MAC addresses and IP addresses can be found under this setting.
Permissions
Administrator level accounts can use Permissions to set access to the Settings app tabs
for general level accounts.

21 CFR Mode: Administrators can disable the “Discard” button from this screen if
desired.
Sound
Play a test sound.
66

Storage
Displays current storage statistics.
Wi-Fi

Turn Wi-Fi on or off and connect/disconnect from a network.
Connect the instrument to a 2.4 GHz or 5 GHz network.
Select the country where the unit is installed in order to ensure the Wi-Fi radio uses thecorrect frequency bands.
DeNovix instruments are compatible with eduroam using login credentials provided byyour institution. See Technical Note 225 on denovix.com for a step-by-step guide toconnect.
Ethernet
Ensure that the Ethernet cable is connected.

Tap the Edit button to configure Ethernet connection.
Contact your local IT department if additional help setting up Wi-Fi or Ethernet is needed.
Display
Includes controls for screen brightness and when the screen sleeps.

Network Folder
The instrument can export to SMB network folders connected to the same network as the
instrument. For best results connect to the network through an ethernet connection,
especially if exporting pdfs and images.

Enter the following information. See DeNovix Tech Note 122 or your IT Department for
additional help.

67•Name - Create a name for your network connection.

•

Server - The IP address of computer or server where the shared folder is located. The
IP can be found in Windows Network Status under “Properties” or byentering ipconfig at the Windows command prompt.

•

Domain name - The domain name when the shared folder resides. From a windows
command prompt enter echo %userdomain%. Do not include slashes orbackslashes.

•

Share path - The share name of the shared folder. In Windows, find this by rightclicking on the shared folder and viewing the properties. The share name should be asingle word. No slashes or backslashes.

The example below shows a correctly shared folder.

•

Mount point (optional) -The path to a subfolder within the main shared folder.
Example input sub1/sub2 is sub1 is a folder inside the main shared folder and sub2
is within folder sub1.

•

User name - The username accessing the share. No slashes or backslashes.

•

Password - Password of the User name account.

Press Connect to connect to the network folder. Press Send Test File to transfer a timestamped text file denovix.txt to the network folder.

Network Printing
Search and add compatible network printers for easy export of hard copy reports.

Email
Email Set-Up•

Ensure that the instrument is connected to Wi-Fi or Ethernet.

•

Launch the Settings app and navigate to the Email section on the left scroll menu.

•

Enable the POP3 option on your Email configuration. Do not use an IMAP account as
messages from IMAP accounts could occupy a significant amount of the
instrument's memory.

See Technical Note 205 on denovix.com for a step by step walkthrough of email setup.
Refer to your IT support group and DS-11 Series Technical Notes on denovix.com if
additional assistance is required.
68

Updater App
Updater is used to update system software and firmware to the most current available
versions. Updates may be downloaded using the Updater app when connected to
Ethernet or Wi-Fi. An Ethernet connection is recommended for software updates.
Updates may also download to a FAT32 formatted USB drive from denovix.com.
Download the update file to the root directly of the USB drive. Do not change the file
name. Insert the USB drive in the device and then launch the Updater app. Follow the
onscreen instructions to update.

Note: The update process may require one or more automatic system reboots.

69

21. 21 CFR App

21 CFR

Compliance Ready Software
DeNovix 21 CFR Part 11 Compliance Ready Software is available for activation on DS-11
Series, QFX and DS-C instruments. An activation code is required and can be purchasedfrom DeNovix or a DeNovix distributor. Once activated, 21 CFR Mode provides a suite ofseamless, integrated controls for electronically signing records, managing user accounts,
configuring the organization and accessing the audit trail. The software enables thefollowing:•

A convenient configuration wizard for easy set up and customization during
activation.

•

User login with unique User ID and password for each user.

•

Operation as a closed system with a single, continuous period of controlled systemaccess.

•Users review results and electronically sign records while logged in. Records can beelectronically signed with a Signature Meaning that is associated with the user’s
assigned Role.

•

Prompt export (and back up) of electronically signed records to a second location
when completing a measurement session.

•

Export of human readable pdf reports and optional raw data such as csv files. The
pdf report includes details of each electronic signature associated with a record.

•

A user interface for viewing stored information but no ability to directly access andalter electronically stored data.

•

Administrator tools to customize and manage the organization’s Roles, Signature
Levels and Signature Meanings.

•

Administrator tools for User Account management including Role assignment,
activation, deactivation, name changes and password resets.

•

An Audit Trail function to automatically log system events and user activities in a
database. If audited, System Administrators can easily search the Audit Trail andexport a human readable .csv report.

70

Activation Wizard Overview
The activation wizard is a step-by-step procedure for setting up an instrument to comply
with your organization’s needs. Default valves are included but are fully configurable
during activation. 21 CFR Mode:•

Each user is assigned to Role•

Each Role has a Signature Level which establishes a rank in the organization•

A set of Signature Meanings must be defined (tested, rejected, approved, etc.)•

Roles are linked to one or more Signature Meanings, meaning that any User who isassigned to a Role can electronically sign a record with one of the available
signature meanings.

•

Once the organization rules are configured, each user is assigned to a Role. Thisestablishes the signature privileges of each user.

Activation Wizard 1/7 - Administrator AccountTo begin, open the 21 CFR app and select an Administrator level account from the
Account selector at the top of the screen. If a user created Administrator account isn’t
selected or none exists, the user is prompted to create a new Administrator account.
When 21 CFR Mode is activated, the open access accounts “General” and “Primary
Admin” are deactivated.

Activation Wizard 2/7 – Enter Activation CodeEnter the twenty-digit activation code and press Apply Code.

Activation Wizard 3/7 - Roles
Users will be assigned to a Role in the final step of activation. In this step set up theRoles for the organization. Each Role includes a value for Signature level. The Signature
Level value establishes a hierarchy in the organization. Users can view data for users attheir Signature Level and below. But they cannot view data for Roles with higher
Signature Level number.

71

Activation Wizard 4/7 – Signature Meaning
Each User, through their assigned Role, will be able to electronically sign records with the
Signature Meanings as defined in this table. Configure the Signature Meanings as
required for the organization but using the add, edit and delete icons. At least one
Signature Meaning must exist.

Activation Wizard 5/7 – Role-Signature Meaning Linking
In this step, set the Signature Meanings for each Role. Select a Role from the table andthen check Include to allow that Role to electronically sign records with that particularSignature Meaning. In the example shown, the Sr. Technician Role can e-Sign records
with Tested, Reviewed and Edit sample name/description Signature Meanings. Any Role
must be linked to at least one Signature Meaning.

72

Activation Wizard 6/7 – Password Rules
Set password rules as desired for the organization. Some requirements are optional.
Minimum password length and account locking after failed attempts to login are
requirements of 21 CFR Part 11 compliant software.

Activation Wizard 7/7 – Existing Users
The final step of the Activation Wizard is to complete the user records for any existinguser accounts that are on the system. Each user must have a User ID, First Name, LastName, Role and a temporary password set in order to complete the wizard. Edit user
accounts by selecting them from the list and then using the edit icon.
Note: This is last opportunity to delete existing user accounts. After 21 CFR activation iscompleted, user accounts may be deactivated, but they may not be deleted.

73

Measurements and Electronic Signed Records
DeNovix 21 CFR compliance ready software enables users to electronically sign results
according to their signature level and permissions established by a system administrator.
Organizations are responsible for establishing standard operating procedures to ensure
users and the organization comply with all facets of the 21 CFR regulations.
Blanks and Sample Measurements must be electronically signed.
Follow app specific instructions for creating methods or generating standard curves if
applicable.

After each measurement, the user must choose to Sign or Discard a result.
•Discard: The result is not saved. SOPs should be established related to the use of
discard to avoid ‘testing into compliance’ scenarios. The Discard button may bedisabled by an Administrator account using the Permissions tab in the Settingsapp.

•

Sign: With the first measurement of each session, the user must verify the user
ID and enter a correct password. Subsequent measurements are signed with theuser ID only.

Measure additional samples until ready to end the session.
DeNovix recommends that the users immediately export signed records and reports
when ending a session. As a reminder, at the end of each measurement session the user
will be asked if they would like to generate a 21 CFR Report for the session.
The 21 CFR Report is a non-editable, human-readable pdf report summarizing data fromall measurements within a session (or selected results within a session or the Data app).
The report includes result information, electronic signature details for each result and theMD5 (hash) value of a csv file of all data included in the report.

21 CFR Reports and csv should be backed up to a secondary location (USB drive, network
folder, hard copy to printer, etc.). The system administrator is responsible for ensuringsystems are properly backed up.
Standard curve replicates do not need to be signed. The values of all replicates used togenerate a standard curve are saved with each result. The user signs the measurement
which binds the sample result to the curve used to generate it.
74

Audit Trail
DeNovix 21 CFR software continually creates an Audit Trail which is a time-stamped log
of events and changes that take place in the system throughout the life of the instrument.
Administrators can search the audit trail to filter the results by date, Event Type, User ID
and Signature Meaning.

Event types tracked include Signature, System, User Account, Record Management andApplication/Machine errors. Some examples of logged events are the electronic
signature of a result, deactivating a user, a failed login attempt, exporting a result andarchiving a record. This list is only representative and is not a complete list of all actions
logged.
Set the filters as desired and press Search to update the result list. Select records andpress “Add to Report”. Move to the Report Tab to see additional information about each
audit trail entry. To export a copy of the Audit Trail as a .csv file, select records, press theexport icon and select the destination.

IMPORTANT NOTE FOR SYSTEM ADMINISTRATORS!
The Audit Trail should be backed up on a regular basis by a System Administrator.
DeNovix recommends that organizations establish procedures to regularly export the full
Audit Trail log via .csv to a backup file location.

75

Archiving
Results that have been previously exported from the instrument may be permanently
deleted through use of the Archiving function in the 21 CFR app. This is the only
mechanism for removing data from the instrument. Prior to removal, the Administrator
should confirm records that will be removed have been properly backed up to anotherlocation. Use the Data app to export additional copies of the electronically signed results
prior to archiving. Archiving immediately and permanently deletes all data associatedwith the signed record. Do not archive a record before confirming a secure copy of therecord exists in a secondary location or has been properly managed according to theorganization’s records retention policies. All Archiving events are captured in the Audit
Trail database.

Filter the results by date, App, User ID and Signature Type as desired. Touch Search to
update the search results. Select desired results and then Add to Report.

The Report tab view shows if a result has been previously exported from the system. Only
results that have been exported can be selected for archiving. Touch the delete icon toinitiate archiving. The system Administrator must enter their password to complete
archiving. The archived records are immediately deleted. Since the record has beenpreviously exported, an additional backup copy is not created at the time of archiving.

7622. 21 CFR Mode - Utility Apps and Functions

User
Accounts

Data

Settings

Updater

21 CFR Mode Instructions
This section describes functionality for instruments that are running in 21 CFR Mode.
Please see the Utility Apps and Functions section for details about how the apps are
configured in Standard mode.

User Accounts App
System Administrators use the User Accounts app to create and manage user accounts
on the device. The app is also used for selecting roles, deactivating users, setting
temporary passwords and changing account information. Each user is required to have aunique User ID and password that meets the organization’s password rules set in the 21
CFR App. All User Account changes are captured in the 21 CFR Audit Trail data.
IMPORTANT: Organizations are responsible for following the strict security
requirements of 21 CFR Part 11 regulations. DeNovix software enables a method ofcompliance, but organizations are responsible for establishing and following
procedures to ensure compliance.

App Structure
User accounts are listed in the left pane of the screen. Within a user’s own account, tabs
in the right pane allow access to User Profile, Emails, Network Folders and Default
settings.

Administrators can access the Profile tab of other users by selecting that user from thelist in the left pane.

77

App Functions
Administrators have the following functions within the User Accounts app.
• Add accounts• Set Account Type• Assign Role
• Change first name or last name• Set Temporary Passwords• Deactivate / Reactivate accounts

Adding Accounts
Choose the + symbol from the left column to add a new user. Assign a User ID and theuser’s information. Create a temporary password for the new user. All users must have aunique User ID.
Account Type•

User – This account type has full access to count apps and permitted utility
apps. User account types do not have any access to Administrator level systemsettings. A user may change first name, last name or password of his/her own
account, but the user cannot change anything related to other user accounts.

•

Administrator – This user type has full access and control over all systemsettings. At least one Administrator account must always be active in 21 CFR
Mode. All Administrator accounts have the same administrative controls on thedevice.

Role

78

Each user must be assigned to an available Role as defined in the 21 CFR App. See 21
CFR App section for configuration details.
Account Passwords•

Passwords are required for all Users.

•

Password must follow the organization rules set in the 21 CFR App (special
characters, length, etc.)•

A user may not reuse a password they have previously used.

•

If a user is unsuccessful logging in over a set number of times (set in 21 CFRapp), the account is locked. An administrator can set a temporary password to
unlock the account.

•

Organizations are responsible for establishing password security procedures toensure compliance with 21 CFR Part 11requirements.

•

Contact DeNovix customer support or your local distributor if the sole
Administrator password is forgotten. Please have the serial number of the
instrument available when requesting help for the reset.

Deactivate / Reactivate an AccountUser accounts may be deactivated by an Administrator. Per 21 CFR Part 11 guidelines, auser account may not be deleted. User activation/deactivation is tracked in the Audit
Trail.

Tab - Email Addresses
Multiple “to” email addresses for exporting results may be set up for each account. The
nickname is used in the drop-down list presented on an export destination dialog box.
Tab - Defaults
Some application specific default settings may be defined on a per account basis.
Launch the Accounts app from the Home screen and then use the drop-down menus toselect the account, the app and the setting of interest.

Note: The default selections for the General Account may not be modified.

Data App
This app allows the user to search for past data by user, date or application. Data canthen be added to the Report and Graph screens for review and export.
Data may be filtered in the following ways from within 21 CFR software:•App, Export status, User ID, Signature Type, date•Once the filter criteria have been selected, tap the Search button at the bottomof the screen. Tap any column header to sort the results list.

•

Highlight the sample(s) of interest and tap the Add to Report button to include
the samples on Results tab pages.

•

All data must be from the same app type for the samples to be added to theReport tab.

•Features and functions previously described for the Result screens apply to thecorresponding Data App Report screens.
79

ExportAll electronically signed data is automatically saved to the onboard memory at the timeof measurement and may be exported as described in the previous section.

When the export function is used data is not deleted.
DeleteThe Delete function is not active for instruments in 21 CFR Mode. Data can only bearchived from the system by an Administrator through the 21 CFR app.

Settings App
See Settings App section in Utility Apps and Functions.

Updater App
This app can be opened by Administrator level user accounts when in 21 CFR Mode.
Updater is used to update system software and firmware to the most current available
versions. Updates may be downloaded using the Updater app when connected to
Ethernet or Wi-Fi. An Ethernet connection is recommended for software updates.
Updates may also be downloaded to a FAT32 formatted USB drive from denovix.com.
Download the update file to the root directly of the USB drive (do not change the filename). Insert the USB drive in the device and then launch the Updater app. Follow the
onscreen instructions to update.
Note: The update process may require one or more automatic system reboots.

8023. Lab Tool Apps

Calculators

Timer

ScreenLocker

Calculator App
Three calculators are included within the app. Use the tabs in the top action bar tonavigate between the options.

Oligo Calculator
This calculator analyzes a user input ssDNA or RNA sequence of interest.
• Outputs include:• Length• Molecular Weight (g/mol)• GC Content• Mass Extinction Coefficient (µg/OD @260 nm): This result may be copied andpasted into the Factor Input field used for nucleic acid concentration calculations inboth the ssDNA and the Microarray apps.

• Melting Temp: For sequences up to 13 nucleotides, the equation used is Tm=(wA+xT) * 2 + (yG+zC) * 4 where w,x,y,z are the number of the bases A,T,G,C in thesequence. For sequences longer than 13 nucleotides, the equation used is Tm= 64.9
+41*(yG+zC-16.4)/(wA+xT+yG+zC). Both equations assume that the annealing
occurs under the standard conditions of 50 nM primer, 50 mM Na+, and pH 7.0.

Scientific Calculator
Use this calculator for standard mathematical and scientific functions.

Dilution Calculator
This calculator is a useful tool to calculate how much of a stock solution should be
added to a buffer solution to result in a final specified solution concentration.
• Both molar and mass units are available. However, conversions between the two typesof units are not enabled.

81

Timer App
This app is a lab tool that allows a user to set two independent timers.
• At the end of a specified period, an alarm will sound.
• Push the Off button to silence the alarm.
• The Timer will work in the background while other measurement apps are in use as
well as when the screen is in the dark screen saver mode.

ScreenLocker
Launch the ScreenLocker app from the Home screen prior to cleaning the touch screen.
This will disable swiping motions from activating other software activities. Tap the homebutton to exit.

8224. Maintenance
Cleaning

RoutineBetweenMeasurements

1. Pipette 2 μL of dH20 onto the bottom sample surface. Lower
the upper arm. Wait 1-2 minutes.
2. Wipe away the water from both the upper and lower sample
surfaces with a dry, lint-free lab wipe.
Use a dry, lint-free lab wipe to remove samples from both thelower and upper sample surfaces.
Use the following procedure to remove sticky solutions (e.g.
proteins) that may have dried down on the sample surfaces.

Additional
Cleaning

1. Pipette 2 μL of 0.5 M HCl onto the bottom sample surface.
Lower the upper arm. Wait 2-3 minutes.
2. Wipe away the HCl from both the upper and lower sample
surfaces with a dry, lint-free lab wipe.
3. Repeat steps 1-2 with 2 μL of dH20.

Guidelines• Use only a dry, soft, lint-free cloth to clean the front screen.
• Do not use a spray bottle to apply water or any other solutions onto any surface of the
instrument as the liquid may damage internal components.
• The use of detergents or isopropyl alcohol as cleaning solvents is not recommended
as they may temporarily alter the hydrophobic nature of the sample surfaces.
• Hint: Launch the ScreenLocker app prior to cleaning the touch screen to prevent
swiping motions from activating other software activities.

Cuvette and Fluorescence Mode Holder Cleaning
The cuvette and FX tube holders may be cleaned of excess dust using canned air or adamp (not wet) lint free cotton swab.
• Do not allow any liquid to drip into the holders as it may damage the internal
components of the instrument.
• Refer to the cuvette manufacturer for guidance on cleaning cuvettes.

Solvent Compatibility
The DS-11 spectrophotometer microvolume sample surfaces are compatible with mostsolvents typically used in life science laboratories.
Exception: Do not use Hydrofluoric Acid (HF) as the fluoride ion will dissolve the quartz
fiber optic cable.
8325. Diagnostics

Diagnostics

FX Diagnostics

Although the DS-11 Series proprietary SmartPath technology enables accurate
microvolume pathlength control and eliminates the need for routine recalibration, labs
may choose to run the Diagnostics app to verify that the instrument is working within
specifications.

DS-11 Self Test
• Ensure that both the upper and lower microvolume measurement surfaces are cleanprior to starting the Self Test microvolume mode assessment.
• For DS-11+ models, remove cuvettes from the holder block and ensure the light path isclear of all obstructions prior to starting the Self Test cuvette mode assessment.
• A spectral plot of the xenon flash lamp intensity and a table that compares measured
versus specified values for a panel of specifications will be displayed. If any of theparameters fail to meet specifications, clean the measurement surfaces as describedin the chapter entitled "Maintenance" and repeat.

Lamp Reset
The Lamp Reset function should only be used when there is concern that a method
optimization was done on dirty sample measurement surfaces.

Microvolume Pathlength Verification
The DeNovix LC-NA verification fluid is supplied as single use vials composed of a nontoxic solution of aqueous nicotinic acid. The solution is used to verify that the
microvolume pathlengths are within specifications.

Procedure
1. Ensure both sample measurement surfaces are clean. Refer to the general cleaning
instructions in the chapter entitled "Maintenance" for more information.
2. Launch the Diagnostics app and navigate to the Verification tab.
3. Enter the lot specific Target Absorbance stated on the ampule in the appropriate field.
4. Add 1 μL of dH2O to the pedestal, lower the arm and click Blank.
5. Wipe the upper and lower pedestals using a dry, lint-free laboratory wipe.
6. Vigorously shake the nicotinic acid ampule to thoroughly mix the solution. Ensure all of
the solution is in the bottom portion of the ampule before opening.
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7. Pipette 1μL of the solution onto the sample surface, lower the arm and click Measure.
8. Wipe the sample off both the top and bottom sample surfaces.
9. Repeat steps 7 and 8 for a total of 5 measurements using fresh aliquots for eachmeasurement.

LC-NA Single Use Ampules•

The LC-NA solution is supplied in single use ampules that should be used
immediately upon opening. Significant changes in concentration and possible
verification check failures may occur if the ampule is opened for longer than one
hour prior to use.

•

Store unopened ampules in a dark, room temperature environment.

•

Always use a fresh vial for each verification check procedure.

•

Do not use parafilm or other methods of sealing an ampule as evaporation may still
occur and result in verification test result errors.

•

Note: Only the LC-NA standard available from DeNovix and its authorized distributors
should be used for the verification check. No other sources of nicotinic acid aretested and validated for use with the DS-11 verification procedure.

Results
A Pass or Fail message will appear in the results box at the bottom of the screen. If the
instrument fails, please clean the surfaces and repeat the test with a fresh aliquot of LCNA.

85

Verification Check Troubleshooting

Issue

Probable Causes/ Solutions

Low AbsorbanceValuesDirty measurement surfaces or improper Blank.
Clean the surfaces, measure a new Blank using fresh source of dH20
and restart the procedure using a new ampule of LC-NA.

Multiple measurements made using the same aliquot.
Use a fresh aliquot for each measurement.
Pipette tips not changed between aliquots.
Use a fresh tip to pipette each aliquot onto the sample surface.
High AbsorbanceValues

The sample surfaces are not adequately cleaned between
measurements.
Wipe both the top and bottom surfaces with a dry lab wipe.
The solution has concentrated due to prolonged exposure.
Use a fresh ampule of solution.
Multiple measurements made using a single 1 ul aliquot.
Use a fresh aliquot for each measurement.

High Standard
Deviations

Pipette tips not changed between aliquots.
Use a fresh tip to pipette each aliquot onto the sample surface.
The sample surfaces are not adequately cleaned between
measurements.
Clean both the top and bottom surfaces between measurements.

86FX- Diagnostics
The FX diagnostics feature can be used for instruments with fluorometer mode or for an
FX Module USB accessory attached to a DS-11 unit.

Procedure
1. Ensure FX sample measurement tube holder is empty and the lid is closed
2. Launch the FX Diagnostics app and push the Start button.

• Follow on-screen instructions regarding tube insertion and orientation.
• The software tests that each LED is firing and each detector is functioning properly.
Results will be reported as Pass/Fail.

8726. Troubleshooting
Quick Help
Most issues concerning accuracy, reproducibility, negative spectra and low nucleic acidpurity ratios are sample or technique related and are resolved by following thesuggestions below:• Establish a new Blank using the appropriate buffer.

• Ensure that the sample isolation procedure is optimized and that samples are purified
when required prior to making absorbance measurements.
• Ensure all solutions are homogenous and well-mixed prior to sampling.
• Ensure sample concentrations fall within the absorbance limits of the instrument. In
the case of fluorescence assays, ensure sample concentrations fall within the reagent
limits as described by the assay manufacturer.
Microvolume Mode
• Ensure both top and bottom microvolume measurement surfaces are clean prior to
making the Blank measurement.
• Always remove sample solutions from both the top and bottom measurement
surfaces using dry, lint-free wipe immediately after each measurement is complete.
• Use calibrated pipettors and properly fitting tips to ensure a full 1 μL aliquot isdelivered to the sample measurement surface. Protein samples sometimes wick up on
the outside of the tip and may not be properly dispensed.
• Use a clean pipette tip and a new aliquot of sample for each microvolume
measurement.

Cuvette Mode
• Use cuvettes with Z heights of 8.5 mm.
• Use quartz or UV transparent cuvettes for UV range measurements.
• Ensure cuvettes are clean prior to use.

• Fill cuvettes to manufacturer's specifications.
• Confirm the mode selection has been changed on the Run screen to the proper cuvettepathlength prior to a measurement.
• Ensure cuvettes are properly inserted following the etched arrow light path.

• Refer to a reagent kit manufacturer for troubleshooting colorimetric assays.

Fluorescence Mode
• Use 200 μL volumes in a clear thin-walled PCR tube

• Avoid introducing air bubbles into the sample solution when mixing samples.
88• Ensure all sample concentrations in the thin-walled assay tubes fall within the limits of
the assay or reagent kit for accurate results.
• Follow assay reagent manufacturers' recommendations regarding temperature,incubation time, and protection from ambient light.

• Follow assay reagent manufacturers' recommendations regarding suggested standard
curve concentrations and data analysis.
• Confirm that the correct LED excitation source was used.
• Confirm that standard concentrations and dilutions were prepared correctly.
• Confirm that the correct concentration units for the standard curve and the unknown
samples were used to calculate the stock concentrations.
• Ensure that the correct optional dilution factor (or μL added in the case of Qubit and
DeNovix assays) is entered into the appropriate Run screen field before ameasurement is made.
• Ensure all samples and standards are treated identically in terms of incubation times
and temperature.
• Minimize assay tube and solution temperature fluctuations as these may impact theaccuracy of the measurement.
• Do not label the side of an assay tube as this could interfere with the sample
measurement.
Additional troubleshooting resources (technical notes and FAQ's) are available at our
website.

Software Errors
Pop-up messages will provide guidance for software-based errors or invalid user actions.
In most cases, simply relaunching the app or restarting the instrument will allow the user
to continue to make measurements. Update the software using the Updater app if
experiencing a reoccurring software error.

Printer and Barcode Scanner
The DS-11 Series is compatible with select label printers* and Opticon OPI 3601 USB
barcode scanners. For accessory product troubleshooting and warranty information,please contact the manufacturer of the product. DeNovix support is limited to thespecific use of the product with a DS-11 Series instrument.
*

Please refer to our website for a list of supported label printers.

8927. Customer Support
DeNovix Inc.
3411 Silverside Road, Hanby Building
Wilmington, DE USA 19810
302-442-6911
info@denovix.com

Please include the serial number of your instrument when contacting Customer Support
by email. If sending Customer Support a Screen Capture or a report .csv file using the DS11 email feature, include your name, institute/company, phone number and return email
address. Please note responses will not be sent directly to the email account used by
the instrument.

From the Diagnostics App use the overflow menu to access the TechSupport filepackage. Include those files, when possible, with a request for support.
Outside of the US, please contact your local distributor for assistance.

Warranty
All product(s) and accessories sold by DeNovix Inc. are under warranty against
manufacturing defects in parts.

Disclaimer
All information in this document is for reference purposes only. DeNovix Inc. makes noclaims that this document is complete or error-free and assumes no responsibility andwill not be liable for any errors, omissions, damage or loss that might result from any useof this document. The information in this document is updated frequently and may be
updated at any time. Visit denovix.com to obtain the latest version.

Instructions for Disposal of Packaging and Waste Equipment
DeNovix encourages customers to locally recycle shipping and packaging materials.
Corrugated cardboard and paper can be recycled wherever it is accepted locally (e.g.,curbside bins, recycling facilities, etc.). For foam and plastics, please contact your local
recycling office for information on how to recycle.
When an instrument has reached its end of life, DeNovix recommends that customers
responsibly dispose of the equipment by following in line with local regulations. Material
construction is available upon request. Visit denovix.com/sustainability for more
information.

Research Use Only
DeNovix Inc. products are for research use only.
Qubit, Quant-iT, PicoGreen and OliGreen are trademarks of Thermo Fisher Scientific and its subsidiaries. QuantiFluor is atrademark of Promega Corporation.

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