Rev Mar 2021

Table of Contents
1. Introduction ..............................................................................................5
2. Set up and Safety .....................................................................................6
3. Software Quick Guides ............................................................................8
Software Icons .........................................................................................8
Software Buttons .....................................................................................9
Software Navigation ..............................................................................10
Top Bar Overflow Functions ...................................................................11
4. Report and Graph Screens ....................................................................12
5. Absorbance Apps: Basic Operation .....................................................15
Typical Absorbance Run Screen ...........................................................17
Best Practices Absorbance Measurements ...........................................19
6. Absorbance Nucleic Acid Apps ............................................................20
dsDNA, RNA and ssDNA .......................................................................21
Microarray ..............................................................................................22
7. Absorbance Purified Protein, Peptide Apps ........................................28
Protein A280 ..........................................................................................29
Labeled Proteins ....................................................................................31
Peptides .................................................................................................33
8. Absorbance Colorimetrics App ............................................................36
Generating a Standard Curve ................................................................37
BCA .......................................................................................................40
Bradford .................................................................................................40
Lowry .....................................................................................................40
Pierce 660 .............................................................................................40
9. Absorbance UV-Vis App ........................................................................41
10.Absorbance OD 600 App .......................................................................432

11.Absorbance Kinetics App .....................................................................45
12.Absorbance Custom Methods Apps ....................................................49
Custom Standard Curve Methods .........................................................50
Custom Formula Methods .....................................................................51
13.Fluorescence: Basic Operation ............................................................53
Best Practices ........................................................................................54
14.Fluorescence: Standard Curve Method Apps .....................................55
15.Basic Fluorometer App .........................................................................62
Excitation Selection and Emission Results ............................................63
16.Data Export and Print Options .............................................................64
Export Options .......................................................................................64
Export Via Email ....................................................................................65
Export to a Network Folder ....................................................................66
USB .......................................................................................................68
Print Options ..........................................................................................70
17.Utility Apps and Functions ...................................................................72
Accounts App .........................................................................................72
Data App ................................................................................................74
Export vs Archive ...................................................................................75
Settings App ..........................................................................................77
Updater App ...........................................................................................80
18.Lab Tool Apps ........................................................................................81
Calculator App .......................................................................................81
Timer App ..............................................................................................82
19.Maintenance ...........................................................................................83
Cleaning ................................................................................................83
Solvent Compatibility .............................................................................843

20.Diagnostics ............................................................................................85
DS-11 Self Test ......................................................................................85
Microvolume Pathlength Verification .....................................................86
Verification Check Troubleshooting .......................................................87
Fluorometer Diagnostics ........................................................................89
21.Troubleshooting .....................................................................................90
Quick Help .............................................................................................90
Software Errors ......................................................................................92
22.Customer Support .................................................................................934

1. Introduction
Product Technology
DeNovix Spectrophotometers / Fluorometers are compact, stand-alone
instruments with a 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 fluorescencemeasurements.
SmartPath™ Technology automatically adjusts the microvolume mode
pathlengths to enable sample measurements across a broad concentration
range. Bridge Testing™ 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 include:• Stand-Alone Design, no-PC required• Hi-Definition 7-inch Touchscreen Interface• 1 μL and Cuvette Full Spectrum UV-Vis Analysis• Four LED Excitation Options• WiFi, Ethernet and USB connectivity

5

2. Set up and Safety
1. Remove all packing materials including the protective cover on the screen.
2. Plug the unit into a 100-240 VAC, 50-60/Hz receptacle using the grounded
power supply (CUI MPN: ETSA120330U-P5P-SZ, Transformer Dest Top 12V
40W, Lead free / RoHS Compliant) included with each unit.
3. For instruments with red LED power indicators, turn on the power switch
located in the back of the instrument. For instruments with green LED power
indicators, press and release the power switch.
The Android™ based operating system will boot up in less than a minute.
4. Use the Shut Down icon (accessed from within each app or on the Home
screen) to do a soft power down.

Cautions
DO NOT REMOVE COVER
No operator serviceable components inside. Refer servicing to qualified
personnel.
The DS-11 is designed for indoor use under the following conditions:Temperature: 15˚ to 35˚ C
Humidity:
35 to 65 %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

6Installation and Safety

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 parle cable d’alimentation et le bloc d'alimentation fournis avec l’appareil.

VCCI (Class B) compliance statement for users in Japan:
This is a Class B product based on the standard of the Voluntary Control Council

for Interference (VCCI) from Information Technology Equipment. If this is usednear a radio or television receiver in a domestic environment, it may cause radio
interference. Install and use the equipment according to the instruction manual.
This equipment has been tested for radio frequency emissions and has beenverified to meet CISPR 22.2 Class B.

Instrument Rear Panel
The DS-11 comes equipped with one Ethernet and three USB ports. The Ethernet
feature is provided for internet connectivity only. The USB ports are used tofacilitate data transfer to a FAT32 formatted USB storage device and connect tothe accessory FX Module. In addition, the USB ports support the use of selected
DYMO printers* and an Opticon OPI 3601 USB barcode reader. USB mouse andkeyboard devices may also be used with the DS-11 FX+ series of instruments.
* Please refer to www.denovix for a list of supported Dymo printers.

7

3. Software Quick Guides
Software Icons
Add

Select All

ExportDeletePurity Ratio Alert

Sort

Edit

Copy

Info

Undo

Paste

Shut Down

The Overflow (top action bar) is used to access secondary features
such as Select Units, Screen Capture, User Guide and Exit.
Progress bars or busy indicators are used to indicate the instrument
is in the process of making a measurement. Please wait until the icon
has disappeared before performing additional actions.
The USB Flash Drive Eject icon appears in the bottom notification bar
when a drive is detected. The software will automatically safely
unmount the flash drive after a screen capture or a report is exported
to the drive. Tap the icon to remove a flash drive when nothing wasexported or saved.
The Quick Print icon is only displayed on Report or Graph screens
when a DYMO label printer is connected to the instrument.
Auto Export status icons are displayed at the top right of a Run
screen. Ensure WiFi is connected prior to making a measurement.

8

Software Quick Guides

Software Buttons
The absorbance apps Blank button is used to establish a reference
absorbance within each measurement app. The graph will not
display a spectrum for a Blank measurement.
The absorbance apps Measure button is used for sample
measurements. It is inactive until at least one Blank measurement
is complete.
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 thefield 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 the lower
right of some screens. All changes made to a selection are
immediate.

9Software Quick Guides

Software Navigation
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 Current Account Tab drop-down menu on the top
action bar in the Run, Report and Graph screens to select a
specific account within an app. Use the Accounts app tocreate and manage accounts.
The bottom bar Back button is used to navigate to the mainlevel of the current app.
The bottom bar Home button is used to navigate to the Home
screen without closing the app.
The bottom bar Recents button is used to as a means ofdisplaying recently used apps. Swipe the app to the left fromthe Recents list will close the app.
The bottom bar Collapse button is used in place of the Backbutton whenever a keyboard is enabled. Use this button todismiss the keyboard.

Notification Bar
Information such as available updates, scheduled system backups reminders
and WiFi connectivity status are located on the bottom action bar adjacent to thedate and time display. Swipe the notification up for details. Tap outside thenotification box to minimize the information.

10

Software Quick Guides

Top Bar Overflow Functions
ScreenCaptureA .jpg may be exported as described in the chapter entitled"Screen Capture and Export" using this option.

ExportSelected
Samples

A .csv file of sample data may be may be exported as
described in the chapter entitled "Screen Capture and Export".
Network printing is also enabled using this option.

ChangeUnits

Concentration units may be changed in some apps using thisoption.

Archive
Selected
Samples

The Archive function exports data as a .csv file to a network
folder or USB flash drive and permanently deletes it from the
instrument.

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
SupportThe 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.

11

4. Report and Graph Screens
The measurement apps generally use a three page structure consisting of theRun, Report and Graph screens. The various screens are accessed either byusing the top tabs or by swiping the touch screen left or right.
The typical Run screen varies significantly between the absorbance and thefluorescence apps. Refer to the "Basic Operation" section for the absorbancemode and the individual fluorescent app sections for more information.

Report Screen• The Report screen list includes application specific data fields for eachsample measured in the current measurement session.
• Tap rows to highlight and select data for export. The Select All /UnSelect All
icons are used to quickly select or deselect all rows.
• The change will be applied to the current Report and Graph screen rows aswell as to the sample information retrieved using the Data app.

12

Report and Graph Screens• Clear highlighted sample records from the both the Report and Graph screensusing the Delete icon. The data is removed from the current report but is stillavailable 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 the chapter entitled "Screen Capture and Export".

Graph Screen• Tap rows to highlight and select 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 the standard curve trend line.
• Color blocks are used as a legend convention.

13

Report and Graph Screens• Highlight a single row and then tap the Edit icon to add or modify a sample
name. The change will be applied to the current Report and Graph screenrows as well as to the sample information retrieved using the Data app.
• Clear highlighted sample records from the both the Report and Graph screensusing 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 will
exported as a .csv file and spectra may be re-graphed using a spreadsheet
chart function. Additional information is provided in the chapter entitled"Screen Capture and Export".

14

5. Absorbance Apps: Basic Operation
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.
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
are reported in 10 mm equivalent absorbance values.

Cuvette Measurements
Refer to the light path arrow as a guide when inserting a cuvette. Use cuvettes
that meet the 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 theBlank button.
2. Insert a cuvette pre-filled with the sample solution. Lower the arm and tap
the Measure button.

15

Basic Operation: AbsorbanceAuto Run Measurements
1. Perform a Blank measurement as previously described and then select theAuto Run 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 and cuvette mode measurements.

Sample Measurement Modes• Measurement mode selections are made using the drop-down menu foundnext to the Measure button on the Run screen.
• 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 thesample 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 .
• The DS-11+ enables the use of 10, 5, 2, 1, 0.5, 0.2 and 0.125 mm pathlength
Cuvette modes.
• Report screens will include actual absorbance values measured using a
specific cuvette pathlength. Graph screens will display all cuvetteabsorbance values normalized to a 10 mm value.
• A new Blank measurement must be made when changing between
microvolume and cuvette modes.

16Basic Operation: Absorbance

Typical Absorbance Run Screen• Blank, Measure, AutoRun and Mode: Use the Blank button when measuring
the reference solution and the Measure button for samples.Tap the AutoRun
box to enable automatic measurements upon lowering the arm. Use the dropdown menu to select either microvolume or cuvette mode measurements.
• Sample Name: Tap the input box to display an on-screen keyboard or use a
Opticon OPI 3601 USB scanner to enter sample names.
• Sample Type and Factor Fields: Displays current sample type and associatedfactors used for concentration calculations. The fields may be fixed or
selectable depending on the application.
• Absorbance Graph: The spectral plot displays data for the current sample
normalized to a 10 mm pathlength for microvolume measurements. Pinch andzoom 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 areprovided within each relevant measurement app chapter.

17

Basic Operation: AbsorbanceScreen Saver• The backlight for the screen will automatically turn off after 10 minutes ofinactivity. Simply tap anywhere on the screen to resume the last function.
• Although the screen is turned off for the screen saver mode, functions suchas the Timer and Kinetics measurements continue in the background. Always
check that these apps are not in use in the background prior to turning off the
instrument.

Mechanism Busy Indicator• A progress bar will be displayed on the screen when the measurement
mechanism is busy.
• Please do not lift the arm, push software buttons or turn the instrument off
while a progress bar or other busy indicator is displayed.

Measurement Sessions• New measurement sessions begin each time an app is accessed from aclosed state or when the account is changed while the application is open.
• In addition, new sessions automatically begin when the number of sample
records on the Report screen reaches 9999.

18

Basic Operation: AbsorbanceBest Practices 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 andbottom 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 withstrong 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. Selectthe Cuvette option using the drop-down menu next to the Measure button andensure the cuvette is inserted in the proper orientation.

19

6. Absorbance Nucleic Acid Apps

dsDNA

RNA

ssDNA

Microarray

The four preconfigured nucleic acid apps are used to quantify nucleic acidsamples 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

Nucleic Acids: AbsorbancedsDNA, RNA and ssDNA
The basic nucleic acid apps are optimized for the factor used to calculate
sample concentrations.

Screen Features• Sample Type: The sample type is used to determine which ng-cm/μL factor isused 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 isavailable from the 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 is what is 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 acidspecies within a sample. It is important to optimize the isolation protocol toensure accurate quantitation.

21

Nucleic Acids:AbsorbanceMicroarray
The Microarray app is used to quantify nucleic acid samples based uponabsorbance values 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 forthis application. 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 is what is 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 the correction factors applied.
• AXXX: The baseline-corrected dye specific analysis wavelength absorbancevalue (e.g A550 when using the Cy3 dye).

22

Nucleic Acids: AbsorbanceDye List
There are 11 preconfigured dye types available for both the Microarray andLabeled Proteins applications. New dye types may be saved using the List Add/
Edit button to the right of the dye list drop-down menu. Refer to the manufacturerof 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 user-added dyes may only be edited or deleted by the accountholder or an administrator account holder.

23

Nucleic Acids:Absorbance

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.

Baseline Correction for Dyes
The software anchors the visual spectrum display to the baseline at 750 nm forall 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 the visual display and the sloping dyebaseline.
• 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 the proper baseline correction is applied.

24

Nucleic Acids: AbsorbanceNucleic Acid Concentration Calculations
A modified Beer-Lambert equation is used to calculate concentrations asfollows: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 in a change in the reported sample concentration. The DS-11 uses a
correction at 340 nm as the default selection. However, the user may elect todefine 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.

25

Nucleic Acids:AbsorbanceTroubleshooting 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 ofdH20 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.

High 260/230

Low 260/280

Dirty measurement surfaces or improper Blank.
Clean the surfaces, measure a new Blank using fresh source ofdH20 or sample buffer. Use the same solution (water or buffer) the
sample is in for the blank measurement.
Dirty measurement surfaces or improper Blank.
Clean the surfaces, measure a new Blank using fresh source ofdH20 or sample buffer. Use the same solution (water or buffer) the
sample is in for the blank measurement.
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.

High 260/230

26

Dirty measurement surfaces or improper Blank.
Clean the surfaces, measure a new Blank using fresh source ofdH20 or sample buffer. Use the same solution (water or buffer) the
sample is in for the blank measurement.

Nucleic Acids: Absorbance

Ratio Alerts
The DS-11 software v3.0 and above displays alerts icons within the dsDNA, RNAand ssDNA apps for samples with purity ratios outside of specified minimum
and maximum limits. Tapping on the icon will pop-up a message with error
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 or an 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 the threshold.

27

7. 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.

28

Purified Protein, Peptides: AbsorbanceProtein A280
The Protein A280 application is used to quantify samples based uponabsorbance 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 be saved using the List Add/Edit button to the right of the sample type dropdown 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 oran administrator account.

29

Purified Protein, Peptides: AbsorbanceBaseline Correction
Bichromatic normalizations correct for baseline offsets due to sample
particulates. If a baseline correction is not used, the sample spectrum may beoffset from the baseline, resulting in a change in the reported sample
concentration. The DS-11 uses a correction at 340 nm as the default selection.
However, the user may elect to define the baseline nm used for specificmeasurements.

Sample TypeE1% at 280 nm for 10 mm pathlength

BSA

6.67

1A=1mg/mL

10

IgG

13.7

E1%
MW & Ext Coeff

User-defined mass extinction coefficient (L gm -1 cm -1) for a 10
mg/mL (1%) solution
User-defined MW (Daltons) and molar extinction coefficient(M -1 cm-1). However, the user may elect to define the baseline nm used for specificmeasurements.
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.

30

Purified Protein, Peptides: AbsorbanceLabeled Proteins
The Labeled Protein application is used to quantify protein samples based uponabsorbance values at 280 nm as well as Dyes and Fluorophores at specificanalysis wavelengths.

Screen Features• Sample Type: The sample type and associated mass extinction coefficients
options include:
Sample TypeE1% at 280 nm for 10 mm pathlength

BSA

6.67

1A=1mg/mL

10

IgG

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 the correction factors applied.
• AXXX: The baseline-corrected dye specific analysis wavelength absorbancevalue (e.g A550 when using the Cy3 dye).

31

Purified Protein, Peptides: AbsorbanceProtein Type List
New Protein types using either user-defined E1% or MW and Ext. Coeff values
may be saved using the List Add/Edit button to the right of the sample type dropdown 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 oran administrator account.

Dye List
There are 11 preconfigured dye types available for both the Microarray andLabeled 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 forall 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 the visual display and the sloping dyebaseline.
• 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 the proper baseline correction is applied.

32

Purified Protein, Peptides: Absorbance

PeptidesThe Peptide app is used for low concentration samples which do not havearomatic 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 dropdown are preconfigured for both the analysis wavelength and thecorresponding E 0.1%.
• Sample type and associated E 0.1% coefficients options include:
Sample TypeE 0.1% at specified nm for 10 mm pathlength

Analysis Wavelengthe215 nm

11.7

215 nm(recommended)

e205 nm

31

205 nm

E0.1%

User-defined mass extinction coefficient (Lgm -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.
• 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 absorbancevalues (e.g A205 or A215).

33

Purified Protein, Peptides: AbsorbanceProtein 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 isdetermined based upon the absorbance value at the analysis wavelength used
for the measurement.

34

Purified Protein, Peptides: Absorbance

Ratio Alerts
The DS-11 software v3.0 and above displays alerts 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 value that 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 or an 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 the threshold.

35

8. Absorbance Colorimetrics App

BCA

Bradford

Lowry

Pierce 660

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

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 theBlank 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 aminimum of 2 standard concentrations. Alternatively, apply a previously
saved curve selected from the drop-down menu.
6. Navigate to the Run screen. Enter a sample name.
• Optional: Enter a dilution factor to be applied to the reported
concentration.
7. Quantitate the sample using the Measure button.Notes:• The Graph Flip button is available on the Run and Graph Screens in the
Colorimetrics and Custom Standard Curve apps. The flip option is not available
when reviewing the results in the Data app. Only the absorbance style graphs will
be displayed.
• Standard Concentrations: Minimum 2, Maximum 8.

36

Colorimetrics: Absorbance

Generating a Standard Curve
1. Use the drop-down menu on the Std Curve screen to select New Curve or toimport 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 pop-up box to enter a list of standard concentrations for the current
measurement session.
• The table enables up to 7 standard concentrations in addition to thepredefined 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 beedited.
3. Measure at least one replicate of each standard concentration byhighlighting the standard concentration row and then tapping the Measurebutton.
• Up to 5 replicates may be measured for each concentration. Use freshaliquots for each 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 be overwritten.
• A minimum of two standards must be measured before the Measurebutton is active on the Run screen.
• Select a standard row or individual replicate then tap the Delete icon todisplay a drop-down list of delete options.
• Use the Undo icon to restore the most recent edit or delete action.

37

Colorimetrics:AbsorbanceLine 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 tocalculate concentrations.
Options include:• Linear• 2nd Order• Interpolation: This option draws a straight line between each point.
Note: The software will extrapolate concentrations for samples withabsorbances 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 andreused at a later date.

38

Colorimetrics: Absorbance• Use the List Add/Edit button to the right of the curve list drop-down menu tosave a curve or concentration list.

Editing a Standard Curve• The curve is in an editable state when the Lock icon is green.
• When a previously saved curve or concentration list is imported, a red Lockicon will appear. Tap the icon to unlock the curve data set to enablemodifications and new absorbance measurements.
• All modifications to a curve (new or saved) are effective immediately. It is
important to save a curve with a new name prior to making any changes if you
do not want to modify the original curve.
• The only way to recall absorbance data for a standard curve is to save theresults as a saved curve before exiting the app.
• Although all accounts may use any previously saved standard curve or saved
concentration list, only the curve account holder or an administrator may
modify or delete 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.

39Colorimetrics:Absorbance

BCA
The bicinchoninic acid assay (BCA assay) is used to quantify protein bymeasuring 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 types of formulations. The particulates may interfere with the shorter
pathlengths used for the microvolume measurements.

Lowry
The modified Lowry assay is used to quantify proteins based upon theabsorbance of tetradentate 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.

40

9. Absorbance UV-Vis App

UV-VisThe UV-Vis app is used to monitor up to 6 specific analysis wavelengths.
Absorbance values for all wavelengths from the user selected wavelength
ranges are saved for each measurement and can be exported as a .csv file using
the Export function from the Report 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 todetermine which pathlength is utilized by the SmartPath® technology for
microvolume measurements. Enter up to five additional wavelengths ofinterest.
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 theOverflow icon to the right of the wavelength list drop-down menu.

41

UV-VisWavelength 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 will automatically save and then clear current results. A new
Blank is required when switching ranges.
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 an moveable cursor initially set atthe analysis wavelength. Moving the cursor allows the user to find theabsorbance value of any wavelength after a measurement is made.
Note: The cursor wavelength absorbance value is a temporary value not savedby the software.

Baseline Correction
The baseline correction normalizes the entire spectrum using the absorbancevalue of the wavelength specified and corrects for baseline offsets due tosample 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 same measurement session.

42

10. 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 userdefined 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 uL 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 FX +.

43

OD 600

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 the optical configuration of the spectrophotometer.
o

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

• Cell Number Conversion Factor: The cell number conversion factor is used toconvert the 600 nm value into the number of cells per mL for the sample bymultiplying the absorbance value by the factor. Cell numbers are reported interms of 1 * 108 cells. The factor must be entered into the appropriate fieldprior to a measurement.
Note: The cuvette mode selection (i.e the path length) must be taken into
account when determining target OD 600 values or entering cell conversion
factors. When making microvolume measurements, the OD 600 values
reported and used for cell number 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 unlessspecified as a user selection.
The baseline correction screen is accessed from the Overflow icon. Once abaseline correction nm is selected, it is applied to all subsequent measurements
within the same measurement session.

44

11. 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 ofthe method.
• 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 dropdown to define additional new methods or edit previously saved methods.

3.

Navigate to the Run screen and tap the Heater button to preheat the cuvetteblock to the selected temperature.

4.

When the Heater temperature field displays the set temperature, insert the
cuvette and 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 when insertinga cuvette into the cuvette block.
•Use a quartz or UV transparent plastic cuvette when using methods that include the UV
wavelength range.

45

Kinetics:AbsorbanceDefine 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
absorbance value at this wavelength will be plotted versus time on the Trend
plot.
• Analysis nm 2: Optional 2nd wavelength of interest for the method. The
absorbance value 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.

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 thedelay. A duration will be rounded down to to the nearest even multiple of theinterval.
Example: Interval = 10 seconds, Duration = 31 seconds
Duration rounded down to 30 seconds.

46

Kinetics: Absorbance

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 are available 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
overshoot the method set point before reaching a equilibrium + 0.5ºC of theset point.
• Timer: This feature is used to monitor the sample solution warm-up time. The
timer is used in a count-up only mode but is not used to track themeasurement time.
• Stop Button: A Stop button replaces the Measure button on the Run screen
during the Kinetics run. Tapping this button will end the measurement andsave all data accumulated up to that point. The Measure button will beavailable when the run is finished.
• 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.

47

Kinetics:AbsorbanceSample Solution Temperature• The solution in the cuvette may not reach the set point as quickly as theheater. Use the Run screen timer as a means of monitoring the elapsed warmup time. Below are estimated warm-up times.
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 15

The times were determined after a 10 mm plastic disposable cuvette filled with water
was inserted into the cuvette block already heated to the method set point. Actual
times may vary and should be empirically determined for each assay protocol.

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

Report, Graph, Trend Screens• Report Screen: Unlike other DS-11 measurement apps, the results displayedin the Kinetics Report screen list are associated with one assay run. Each timea new assay run is initiated, the previous results will be saved and thencleared from the Report, Graph and Trend screens. The cleared data may beaccessed using the Data app.
Note: It is normal for the software to sometimes experience minor delays inreporting kinetics data information relative to the actual measurement time
point. The actual time each measurement is initiated is what is reported in the
Elapsed Time field.
• Graph Screen: Displays the absorbance for the method-defined wavelength
range for each 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 forexport or screen capture.

48

12. 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 ofthe method.
• 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 accountholder 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.

5.

Measure a fresh aliquot of sample using the Measure button.

49

Custom Methods:AbsorbancePrimary Settings
Each new method requires a unique name. In addition, the following parametersmust 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 todetermine which path length is utilized by the SmartPath® technology for
microvolume measurements.

• Baseline nm: A baseline correction wavelength is required for the Standard
Curve methods but not for the Formula Methods. Bichromatic normalizations
correct for baseline offsets due to sample particulates. If a baseline correction
is not used, the sample 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
requires that 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 Generatinga Standard Curve in the chapter entitled "Colorimterics".
• Standard Curve methods function the same way as preconfigured
Colorimetrics apps.

50

Custom Methods: Absorbance

Custom Formula Methods
In addition to the primary analysis wavelength, the Formula Methods app
enables the user to include up to 4 additional results for each measurement.
The result fields may be used to monitor additional specific wavelengths or havethe 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:
Function

Description

Numerical Operations+ add - subtract * multiply ÷ divideA(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

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

• Advanced: When checked, this feature allows the user to designate that themethod uses a Savitzky–Golay filter instead of the default boxcar method tosmooth data.

51

Custom Methods:Absorbance

Formula Guidelines• Use the A(x) button on the input screen to use the absorbance value result ofa specific wavelength in the formula. Enter the wavelength within theparenthesis.
Example: A(260)• Check that closed sets of parenthesis 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 thesoftware.
Example: A(260)/A(280) is correct while = A(260)/A(280) is incorrect.

• The software automatically applies the baseline correction specified in themethod 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 IQ/OQ 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.

52

13. Fluorescence: Basic Operation
DeNovix Spectrophotometer/Fluorometer software includes both absorbanceand fluorescence apps. The fluorescence app icons will appear on the first pageof the Home screen for the DS-11 FX and DS-11 FX+ models. The inactive
versions of the icons will appear on the second page for DS11 or DS-11+ units
when a FX Module USB accessory is not detected.
The table below lists the four LEDs included in all FX models. Users must selectthe appropriate 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 back USB ports.
2. Insert a micro tube pre-filled with the fluorescent solution. Close the coverand tap Measure.
Notes:• Use clear thin-walled 0.5 mL plastic PCR tubes only
• Measure 200 µl volume samples.

53

Fluorescence Basic Operation

Best Practices• Ensure all sample concentrations in the thin walled assay tubes fall within thelimits 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.
• 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 the accuracy 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.

54

14. 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 avariety of assay. The end user is responsible for selecting the proper choicebased on the analyte that will be used for quantification.

FluorodsDNA•DeNovix dsDNA Broad Range•DeNovix dsDNA High Sensitivity•DeNovix dsDNA Ultra High Sensitivity•Quant-iT™ PicoGreen•Quant-iT™ dsDNA HS•Quant-iT™ dsDNA BR

FluoroRNA•DeNovix RNA Assay•Quant-iT™ RiboGreen•Quant-iT™ RNA HS•Quant-iT™ RNA BR•Qubit™ RNA HS

FluorossDNA•Quant-iT™ OliGreen•Qubit™ ssDNA•Quantifluor ssDNA

FluoroProtein•Quant-iT™ Protein•Qubit™ Protein•Qubit™ dsDNA BR•Qubit™ dsDNA HS•Quantifluor dsDNA•Quantifluor One
dsDNA•Qubit™ RNA BR•Quantifluor RNA•Quant-iT™ microRNA•Qubit™ microRNA

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

55

Standard Curve Methods: Fluorescence

Quick Protocol
1. Launch the app from the Home screen.
2. Select the LED using the drop-down menu on the Run screen.
3. Generate a new curve:•

Insert the standard (200 uL in a thin walled PCR tube) into the sample
holder and lower the cover. Measure at least one replicate for aminimum of 2 standard concentrations•

Alternatively, import a saved curve or list of sample concentrations

4. Tap the Samples radio button. Enter a sample name.
• Optional: Enter a 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 Qubit assays will have predefined standard concentrations and specified
units.

56

Standard Curve Methods: Fluorescence

Run Screen- Assay and Curve Selections
Excitation Source (LED) and Assay Selection• Select an LED from the drop-down menu in the left panel. The user mustchoose the proper LED for the analyte in use (SW V3.52 and later).
• New assays may be entered using the List Add/Edit button.
• User defined assays may be used by all accounts but may be modified ordeleted only by the account owner.

Curve Options
Generate New Curve• Choosing this option will pop-up a dialog window used to enter theconcentration 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 thetime of the assay.
• Trend line analysis options and concentration units used may be changed
using the advanced options button.
• Blank: If selected, the first row in the standards table is used to measure aBlank.The average RFU value of the blank measurements will be
subtracted from all standard and sample measurements. If the Blank is
not selected, the initial concentration for preconfigured assays will be set
to 0.00. This standard is typically 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 graph origin (0,0).

57

Standard Curve Methods: Fluorescence

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 tosave the selection with a new name prior to making any changes if you do notwant to modify the original curve or standards list. Changes to a curve do notaffect previously measured samples.
• Although all saved lists and saved curves are available for use by all accounts,
only the account holder may modify the selection.

58

Standard Curve Methods: Fluorescence

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 thetable.
• The Save button will pop-up the Save Values window. Either concentration
values or concentration 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 automatically saved 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 the trend line.

59Standard Curve Methods: Fluorescence

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 thestandard curve trend line. Results are reported in terms of the units used toderive the trend line.
• The Optional Dilution Factor (or the µl Added value for Qubit™ assays) will beapplied 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 the time of the measurement.

60

Standard Curve Methods: Fluorescence

New Standard Curve Assays/Methods
Each new method requires a unique name. In addition, the following parametersmust 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 thefour excitation sources and will report the associated RFU in the colorcoded boxes• Some fluorophores do not exhibit significant fluorescence unless boundto a protein or nucleic acid. It may be necessary to set up an assay
reaction to best use the LED Wizard.
• The standard curve assay methods use one excitation source todetermine the concentration 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 as well as the standard curve units.
Although all accounts may use any saved method, only the method accountholder or an administrator may modify or delete the new method.

61

15. 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 theuser to excite a sample with one LED and get 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. Insert the standard (200 μL in a thin-walled PCR tube) into the FX mode
sample holder.
4. Optional: Create and Save a used defined method (LED selection and user
defined assay name).
5. Optional: Enter a sample name.
6. Tap the Measure button.

62

Basic Fluorometer

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 the emission results for theblue, green and red channels will be reported. If the green LED is selected,
only the green and red channel results will be reported.
• New fluorophores may be entered using the List Add/Edit button.
• 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 LED that resulted in
the largest RFU at its detector will automatically be chosen as the LED forthe method.

63

16. Data Export and Print Options
Export Options
The data associated with highlighted samples on a Report or Graph screen may
be exported via email, sent to a network folder or saved to a FAT32 formatted
USB flash drive as .csv files.
• Data may be automatically exported to a network folder after every
measurement. Refer to the "Network Folder Set-up" section for more
information.
• To open an exported .csv file on a computer, the DeNovix instrument and thecomputer must both be set to use either period or comma number formats.
The DS-11 FX number format is determined by the language selected using
the Settings app.

Export Formats
Standard Formats• 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.
Custom Formats• User specific formats may be defined using the Export Formats option
accessed from the Report screen Overflow menu.
• The format used when exporting results is selected at the time of the export.
Accounts other than the General Account may set a user-defined format as
the default selection using the Accounts app.

64

Data Export and Print

Defining a New Format:• Provide a title for the format.
• Hold the arrow icon and drag a column up or down to change the order of thecolumns.
• Touch on the column name and swipe it left or right to exclude or include it in
the exported report.
• Tap on the input field to change the name of a column header in the exported
report.

Graph Screen Exports• Selected sample results exported from an absorbance app Graph screen
follow the same format as when exported for the Report screen. Graphs are
not exported as part of the .csv file.
• Use the Screen Capture option to export the current graph via email or to savethe .jpg image to a network folder or a FAT32 formatted USB flash.

Export Via Email• Screen captures as well as data .csv files may be exported via email.
• Use the Account app Overflow Address Book function to save frequently used
recipient email addresses.
• It is recommended that a new, dedicated POP3 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 frombeing stored on the unit.

65

Data Export and Print

Email Set-up
1. Ensure that the instrument is connected to WiFi or Ethernet.
2. Swipe the Home screen to the left to navigate to the second page, launch the
Email app and follow the prompts using the Manual setup option.
3. Input Incoming Server Information:• Select the POP3 option on the Account Types screen. Do not use an IMAP
account as messages from IMAP accounts could occupy a significant
amount of the instrument's memory.
4. Set the inbox checking frequency to "Never" on the Account Options screen.
The DS-11 email should be used only to export data and screen captures.
5. Input Outgoing Server Information:• Use settings appropriate for the lab email server.
6. Enter a name to display on outgoing messages.
Refer to your local IT support group if additional assistance is required.

Export to a Network Folder• Screen captures, data report .csv files, as well as instrument backups anddata archive files may be sent to a selected network folder.
• The two supported transfer options include Server Message Block (SMB) andFile Transfer Protocol (FTP).
• Use the following apps to manage network folder options on the DS-11 FX:
Settings App

66

Data Export and Print• Permission to setup a network folder for the General Account as well as
standard user accounts are enabled or disabled by an administrator using
the Permissions option in the Settings app. "Enabled" is the default
selection.
Accounts App• Network folder paths are defined and saved on a per user account basis
from the Accounts app. The primary Administrator network folders areused only for the Backup and Restore function in the Settings app.

Network Set-up
1. Contact your local IT group to confirm that you have access to a local server
or FTP site. Ensure that the instrument is connected to WiFi or Ethernet.
2. Launch the Accounts app and select a user account.
3. Use the top drop-down menu in the right pane to select the Add New
Network Folder function.
4. Use the List Add/Edit button to add a network folder to the drop-down menu.
5. Select either the SMB or FTP option.
6. Enter a nickname for the network path. This is the name displayed in all
drop-down menus referencing the network folder.
7. Enter the server computer's host name. Contact your local IT group for
additional information.
8. Select log-in option. Contact your local IT group to request log-in credentials.
• Log in: Enter the network folder username and password required toaccess the selected network folder.
• Anonymous: No user name or password required.

67

Data Export and Print• File (SMB only): Upload a configuration file (file extension .prp ) from a
USB device. Note: If a username or password is entered that is different
from information contained in the config file, the manually typed
information will be used in validating the path access. Refer to http://
jcifs.samba.org/src/docs/api/overview-summary.html#scp for additional
guidance.
9. Use the Browse button to locate and select a specific folder path.
10. Use the Auto Report checkbox to enable automatic export of sample data
after every measurement.

USB• Screen captures as well as data .csv files may be saved to a FAT32 formatted
USB flash drive.
• The USB Flash Drive Eject icon appears in the bottom notification bar when adrive is detected. The software will automatically safely unmount the flash
drive after anything is written to the drive. If not removed, the software willautomatically remount the flash drive when another write operation is
performed.
• Please wait for the “OK to remove” toast message to appear before
removing the drive.Tap the icon to safely remove a flash drive whennothing was exported or saved. Failure to follow these instructions may
result in the flash drive becoming unrecognizable to the instrument.
• There are three USB ports on the back of the instrument although only one
storage device is recognized at a time. The two additional ports may be used
for the FX Module accessory as well as for selected DYMO printers andbarcode readers.

68Data Export and Print

Auto Export Icon
When the auto export feature is selected, a status icon will appear at the top
right of the screen after the first measurement.

Export in Progress

Export CompletedExport Failure• Automatic export of every sample measurement to a network folder is enabled
on a per user account basis.
• The auto export feature may only be selected for one saved network folder peruser account.
• Automatic exports will be stored in a single file per app type per user accountper day.
• When selected, the auto export will apply to all measurement apps used by theapplicable account.
Note: All sample data is saved to the instrument even if automatic exports faildue to server connectivity issues.

Troubleshooting Tips
• Confirm that there is WiFi or Ethernet connectivity. Use the Browser app on thesecond page of the Home screen to confirm connectivity or check theconnectivity status icon on the right of the bottom navigation bar.
• Confirm that the log in credentials are valid for the network folder option
selected and that the hostname is correct.
• For internet connectivity issues, network folder access failures and all otherserver related issues, contact your local IT support group.

69

Data Export and Print

Print Options
The DS-11 FX software supports printing to networked printers or to selected
DYMO printers*. All Dymo print-outs are in black and white.
*Please refer to www.denovix for a list of supported Dymo printers.

WiFi and Networked Printers
Screen shots as well as selected sample data and graphs may be printed to both
Wifi enabled and networked printers.
• Use the Overflow menu to select either Screen Capture or Export Selected
Samples to bring up a dialog box with Network Printer as a radio button
option.
• Selecting this option will display a preview of the print-out along with manycustomizable options.
• To select a printer, ensure that the instrument has WiFi or Ethernet
connection and then tap the first item listed under Printer Options. This willbring up a list of available printers. If no printers are listed, tap the Network
Printers icon in the left pane to search for nearby printers.
The current software supports approximately 90% of printers on the market.
DeNovix will continue to add new drivers to accommodate as many new printers
as possible in future software updates but cannot guarantee compatibility withall printers.
Please contact DeNovix or your local distributor for a list of recommended
printers if your current printer is not compatible with the software.

70

Data Export and Print

DYMO Printers• The software enables the use of three DYMO paper or label sizes:• 4x6 labels (DYMO 4XL only) and 2.5 inch paper rolls are used to print
screen captures and selected sample results from the Report or Graph
screens.
oReport and Graph print column formats will be as shown on the
instrument display.

• 1 x 0.5 inch labels are used to print sample names, sample
concentrations, units and the date on individual labels suitable forstandard microfuge tubes.
oWhen used with the Colorimterics or Custom Standard Curves app,the concentration printed is the dilution factor applied recalculated
value.

• A Quick Print button will be displayed on the Run, Report and Graph screens
when a DYMO printer is detected. Label sizes may be selected by tapping theprinter icon displayed next to the date and time in the bottom notification bar.
• Although sample names may include up to 48 characters, the DYMO printed
label will print 2 rows of characters per sample name. The exact number ofsample name characters may vary depending on the language in use.

71

17. Utility Apps and Functions

Accounts

Data

Settings

Updater

Accounts App
User accounts manage default settings within specific apps as well as saved
sample and dye types, wavelength lists and user methods. Accounts are also
used as a means of segregating data when performing searches in the Data app.
The Add New Network Folder function is accessed from a drop-down menu on
the right side of the screen. The Address Book function accessed from theOverflow menu in this app allows users to save frequently used recipient email
addresses for easy reference.

System Accounts
There are two preconfigured system accounts built into the software:• Primary Administrator• This account is used to manage instrument settings. It is not used within
the measurement applications.
• The primary administrator account is not initially password protected. A
password may be applied at any time. Contact DeNovix if help is required
to reset the primary administrator account password.
• 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.

72

Utility Apps

User Added Accounts
All added administrator or standard user accounts may be password protected.
• Administrator Accounts• An administrator level account may only be created by anotheradministrator.
• Administrator accounts may modify or delete user entries of any sortcreated from within any account.
• Administrators may change the password for any account as well as
delete any account.
• Standard Accounts• Any user may add a standard level account.
• Standard accounts may only modify or delete sample or dye types,
wavelength lists or user methods created from within their account.
If an account is deleted, all associated sample and dye types, wavelength lists
and user methods are still available for general use unless deleted by anadministrator.
Contact the holder of an administrator account if a standard user accountpassword is forgotten. Contact DeNovix customer support or your local
distributor if the Primary Administrator password is forgotten. Please have theserial number of the instrument available when requesting help for the Primary
Administrator password reset.

App Default Selections
Some application specific default settings may be defined on a per accountbasis. Launch the Accounts app from the Home screen and then use the dropdown menus to select the account, the app and the setting of interest.
Note: The default selections for the General Account may not be modified.

73

Utility Apps

Data App
This app allows the user to search for past data using either a Advanced Searchor Quick Search option. Data can then be added to the Report and Graph screens
for review and export. In addition, data may be archived from the Search Screen.

Search Options• Data is automatically filtered based upon the Account selected using the tabon the top action bar.
• The Advanced Search allows multiple filters to be applied in a single search.
The Quick Search option enables the user to filter by a single criteria in
addition to the automatic Account filter.
• Kinetics and Diagnostics results are not accessible using Quick Search.

74

Utility Apps

• 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 the Report and Graph screens. Blank measurements may be
included in the list but will not provide any absorbance data.
• All data must be from the same app type for the samples to be added to theReport or Graph screens.
• Note: The Data app does not include a Graph screen for fluorescence
apps.

Export vs Archive• All data is automatically saved to the DS-11 FX onboard computer database at
the time of measurement.
• The Auto Export feature is available when a network folder is set-up using
the Accounts app.
• The Export Selected Samples function available from the Report and Graph
screen overflow menus creates a .csv that can be emailed, sent to a network
folder or saved to a FAT32 formatted USB flash drive.
• When the export function is used, the data is not deleted from thedatabase and can be accessed using the Data app.
• Only one Kinetics run at a time may be added to a Report for export fromthe Data app.

75

Utility Apps

• The Archive Selected Samples function available from the Run and Report
screen overflow menus creates a .csv file with sample data that can beexported to a folder entitled ds11 on a FAT32 formatted USB flash drive or
saved to a network folder.
• When the archive function is used, the data is permanently deleted fromthe instrument database and cannot be restored to the instrument.
• Multiple Kinetics runs may be archived in a single action.
• The archiving privilege for standard accounts is enabled or disabled using theSettings app. When disabled, only administrative accounts may archive data.
• The storage capability of the DS-11 FX is sufficient for several years of data
for a lab with average use. Therefore, it is recommended that the archiving
function be used only as an infrequent method of deleting old data from theDS-11 database. Although archiving a large amount of data may take aconsiderable amount of time, the archive process continues to work evenwhen the interface goes to sleep after 10 minutes of no user activity. Touchthe screen to wake-up the user interface and update the progress message.
• Use the Cancel button to stop the archive button. Samples already copied up
to the stop point may be deleted from the instrument at the user's discretion.

76

Utility Apps

Settings App
The Settings app may be found on the second Home screen page. Only
administrator accounts may access and change settings.
The app provides access to the following functions:

Backup and Restore• The backup process exports a copy of all user-defined app settings, methods,
dyes, sample types, email addresses, shared folder paths, user accounts andsample results to either a USB flash drive or a network folder.
• Backup files include a DeNovix specific extension and may not be opened on
a computer. The files may be restored back onto the DS-11 at any time.
• Automatic backup reminders may be enabled using the checkbox on the
Backup screen.
• The restore function is used to recover user defined app settings, methods,
dyes, sample types, email addresses, shared folder paths, user accounts andall sample results saved at the time of the backup. There are two options:• Recover All: Restores user defined app settings, user entered methods,
user added dyes and sample types, email addresses, shared folder paths
and saved user accounts as well as previous sample results. All new
methods, sample and dye types, emails addresses, network folders, user
app settings and data results accumulated since the time of the back-up
will be overwritten during the restore process.
• Recover User Info Only: Use this option to recover settings, methods,
dyes, sample types, email addresses, shared folder paths and user
accounts. This option will not restore sample data or overwrite new data.

77

Utility Apps

Date/Time• Select manual or automatic date and time options.

Language• Although the Android system provides translations for some routine
functions in many languages, the majority of the app specific text will beavailable in a limited number of language options.
• The DS-11 number format is determined by the language selected.
• Exit all apps before changing languages.

Network Information• The WiFi and Ethernet media access control addresses can be foundunder this setting.

Permissions• This selection is used to enable the following options:
Archive: Use this selection to enable or disable all standard accounts,
including the General Account, to archive (delete) data from the
instrument. Refer to the Export vs Archive section for additional
information regarding archiving.
Automatic Updates: Use this selection to enable or disable automatic
updates of the software.
Network Folder: Use this selection to enable or disable the generalaccount and/or standard user accounts to set-up network folders fordata export/archive and system backups.

78

Utility AppsSound
• Volume controls are available for media and timer alarms.

Storage• Displays storage statistics.

WiFi
To enter static IP addresses :1. Ensure the WiFi is on. Select WiFi from the Settings list.
2. Tap the Add icon on the right side of the top action bar.
3. Dismiss the keyboard using the chevron on the bottom action bar.
4. Select the Show Advanced Options checkbox.
5. Select Static using the IP settings drop-down.
6. Enter the appropriate information and tap Save.

Ethernet
To enter static IP addresses :1. Ensure the Ethernet cable is connected. Select Ethernet from theSettings list.
2. Tap the name of the connection. Use the drop-down menu to selectStatic. Enter the appropriate information and tap Apply.
Note: WiFi will take precedence over the Ethernet when both are connected.
Contact your local IT department if additional help setting up WiFi or Ethernet
static IP addresses is needed.

79

Utility Apps

Updater App
This app is used to update all apps to the most current available versions. The
latest updates are available at www.denovix.com. For instruments without
internet access, a zip file with the latest updates may be downloaded from thewebsite onto a FAT32 formatted USB flash drive.

Procedure

If the DS-11 is connected to the internet via WiFi or Ethernet proceed to step 3.

1. Download the required packages from the www.denovix.com website directly
to the root level of the flash drive. Do not unzip the file folders.
• The blue icon app requires both the Automated Updater (ds11current.zip)and the Latest Software Version (ds11latest.zip) packages.
• The yellow icon app uses only the Latest Software Version(ds11latest.zip) package.
2. Insert the USB device into one of the ports located in the back of the DS-11.
3. Shut down all open apps.
4. Swipe to page 2 of the Home screen and launch the Updater app.
• Blue icon version of the app:
• Press the Check for Updates button. Follow the onscreen directions to
Install the new yellow icon version of the Updater app.
• Once the yellow Updater icon appears on the Home screen, relaunch theapp to automatically update all other apps.
5. Click OK if a message is displayed that indicates new firmware is required. Do
not turn off the power to the instrument during the 10- to 15 second firmware
update process.
Note: Some installed apps are used for important background system functions
and will not be visible on the Home screen.

80

18.Lab Tool Apps

Calculators

Timer

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

Oligo Calculator
This calculator analyzes a user-inputed 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 copiedand pasted into the Factor Input field used for nucleic acid concentration
calculations in both 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 the sequence. For sequences longer than 13 nucleotides, theequation used is Tm= 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC). Bothequations assume that the annealing occurs under the standard
conditions of 50 nM primer, 50 mM Na+, and pH 7.0.

81

Lab Tool Apps

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 types of units are not enabled.

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 for a maximum of 90
seconds.
• Push the Off button to silence the alarm.
• The alarm can be acknowledged via the notification bar or by going back to
the Timer app.
• 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.

82

19. 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 notrecommended as they may temporarily alter the hydrophobic nature of thesample surfaces.

83

Maintenance

ScreenLocker App
Launch the ScreenLocker app from page 2 of the Home screen prior to cleaning
the touch screen. This will disable swiping motions from activating othersoftware activities. Tap the Droid icon three times to unlock the screen.

Cuvette and Fluorescence Mode Holder Cleaning
The cuvette and FX tube holders may be cleaned of excess dust using canned
air or a damp (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 most solvents typically used in life science laboratories.
Exception: Do not use Hydrofluoric Acid (HF) as the fluoride ion will dissolve
the quartz fiber optic cable.

Customer Support
Contact DeNovix Customer Support at 1-302-442-6911 or info@denovix.com if
additional help is required. Please include the serial number of your instrument
when contacting Customer Support by email.
Outside of the US, please contact your local distributor for assistance.

8420. Diagnostics

Diagnostics

FX Diagnostics

Although the DS-11 FX propriety 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 areclean prior to starting the Self Test microvolume mode assessment.
• For DS-11+ models, remove cuvettes from the holder block and ensure thelight path is clear of all obstructions prior to starting the Self Test cuvettemode assessment.
• A spectral plot of the xenon flash lamp intensity and a table that comparesmeasured versus specified values for a panel of specifications will be
displayed. If any of the parameters fail to meet specifications, clean themeasurement surfaces as described in the chapter entitled "Maintenance" andrepeat.

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

85

Diagnostics

Microvolume Pathlength Verification
The DeNovix LC-NA verification fluid is supplied as single use vials composed ofa non-toxic solution of aqueous nicotinic acid. The solution is used to verify thatthe microvolume pathlengths are within specifications.

Procedure
1. Ensure both sample measurement surfaces are clean. Refer to the generalcleaning 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 theappropriate 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.
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 foreach measurement.

86Diagnostics

Verification Check Troubleshooting
Issue

Probable Causes/ Solutions

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

87Diagnostics

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
20 minutes prior to use. Store unopened ampules in a dark, room temperatureenvironment.
• Always use a fresh ampule 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 are tested 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 thescreen. If the instrument fails, please clean the surfaces and repeat the test witha fresh aliquot of LC-NA.

Technical Support
Contact DeNovix Customer Support if additional help is required. For US
customers, please email the results directly to info@denovix.com using the
Diagnostics app Overflow Tech Support function. Include your name, phone
number, institute/company, and return email address. Please note responses will
not be sent directly to the instrument email account.
The Tech Support email includes encrypted files for the DeNovix technicalsupport team.
Outside of the US, please contact your local distributor for assistance.

88

Diagnostics

Fluorometer Diagnostics
The Fluor Diagnostics app is used to confirm that the LED excitation sourcesand detectors are functioning properly.

Procedure
1. Ensure sample measurement tube holder is empty and the lid is closed
2. Launch the FX Diagnostics app and push the Start button.
• The software tests that each LED is firing and each detector is functioning
properly. Results will be reported as Pass/Fail.

Technical Support
Contact DeNovix Customer Support if additional help is required. For US
customers, please email the results directly to info@denovix.com using the FXDiagnostics app Overflow Tech Support function. Include your name, phone
number, institute/company, and return email address. Please note responses will
not be sent directly to the instrument email account.
The Tech Support email includes encrypted files that can only be opened by
DeNovix technical support team.
Outside of the US, please contact your local distributor for assistance.

8921. Troubleshooting
Quick Help
Most issues concerning accuracy, reproducibility, negative spectra and low nucleic
acid purity ratios are sample or technique related and are resolved by following
the suggestions 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 cleanprior 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 iscomplete.
• 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.

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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 theproper cuvette pathlength 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.
• Ensure all sample concentrations in the thin walled assay tubes fall within thelimits 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 performed correctly.
• Confirm that the correct concentration units for the standard curve and theunknown samples were used to calculate the stock concentrations.
• Ensure that the correct optional dilution factor (or uL added in the case of
Qubit® assays) is entered into the appropriate Run screen field before ameasurement is made.

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Troubleshooting• 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 the accuracy 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 FAQs) are available atwww.denovix.com.

Software Errors
Pop-up messages will provide guidance for software-based errors or invalid user
actions. In most cases, simply relaunching the app will allow the user tocontinue to make measurements. Update the software using the Updater app if
experiencing a reoccurring software error.
Contact DeNovix Customer Support 302-442-6911 or info@denovix.com if
additional help is required. Please include the serial number of your instrument
when contacting Customer Support by email. The serial number may be foundon the bottom of the instrument.
Outside of the US, please contact your local distributor for assistance.

Printer and Barcode Scanner
The DS-11 FX is compatible with selected DYMO printers* and Opticon OPI 3601
USB barcode scanners. For accessory product troubleshooting and warranty
information, please contact the manufacturer of the product. DeNovix support islimited to the specific use of the product with a DS-11 FX instrument.
*Please refer to www.denovix for a list of supported Dymo printers.

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22.Customer Support
DeNovix Inc.
3411 Silverside Road, Hanby Building
Wilmington, DE USA 19810
302-442-6911
info@denovix.com
www.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 DS-11 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. Outside of the US, pleasecontact 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 no claims that this document is complete or error-free and assumes noresponsibility and will not be liable for any errors, omissions, damage or loss
that might result from any use of this document.

Research Use Only
DeNovix Inc. products are for research use only.
"Android is a trademark of Google Inc. Qubit, Quant-iT, PicoGreen and OliGreen are trademarks of Thermo Fisher
Scientific and its subsidiaries. QuantiFluor is a trademark of Promega Corporation."93