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DeNovix DS-11 User Manual

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DS-11 Spectrophotometer
User Guide
Rev June 2013

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Summary of Contents for DeNovix DS-11

  • Page 1 DS-11 Spectrophotometer User Guide Rev June 2013...

  • Page 2: Table Of Contents

    Table of Contents Introduction ....................Installation and Safety ................. Basic Operation .................... Software Quick Guides ................Software Icons ..................Software Buttons ..................Software Navigation ................Tab and Overflow Functions ..............General Screen Features ................Run Screen ................... Report Screen ..................Graph Screen ..................
  • Page 3 ..................... Calculators .................... Timer ..................... Maintenance ....................Cleaning ....................Troubleshooting and Diagnostics ............. Quick Help ..................... Software ....................Printer and Barcode Scanner ..............DS-11 Self Check .................. Microvolume Pathlength Verification ............. Verification Check Troubleshooting ............Customer Support ..................Contact ....................

  • Page 4: Introduction

    1. Introduction Product Technology The DeNovix DS-11 Spectrophotometer is a compact instrument with an integrated processor and a high-resolution touchscreen. The software utilizes application specific icons along with the Android operating system to provide an intuitive, easy-to-use spectrophotometer for microvolume absorbance measurements.

  • Page 5: Installation And Safety

    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: 35-65 % Use only the power supply provided with the instrument.

  • Page 6: Basic Operation

    3. 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 the bottom and top sample surfaces using a clean, dry lab wipe.
  • Page 7 Basic Operation Sample Measurement Modes • The measurement mode is displayed on the top bar of all measurement applications. • All measurements are reported in 10 mm equivalent absorbance values. • The Microvolume mode uses 1.0 μL samples pipetted onto the sample surface.

  • Page 8: Software Quick Guides

    4. Software Quick Guides Software Icons The Overflow icon is used to access secondary features and selections. The Select All icon is used to highlight all samples in a list. Use the Undo icon to restore the most recent edit or delete in tables and lists.

  • Page 9: Software Buttons

    Software Quick Guides Software Buttons Blank The Blank button function is used to establish a reference absorbance within each measurement app. The absorbance graph will not display a spectrum for a blank measurement. The Measure button is used to take sample absorbance Measure measurements.

  • Page 10: Software Navigation

    Software Quick Guides Software Navigation Home Screen Apps Applications are launched using Home screen icons. Swipe the Home page to the left for additional icons. Up and Back Button The bottom bar Back button is generally used to navigate to the main level of the current app. If accessed from the main level of an app, the button will bring up an Exit app dialog box.

  • Page 11: Tab And Overflow Functions

    Report and Graph screens. A .jpg of the current screen of the current page may be Screen emailed, saved to a USB device or printed to a DeNovix Capture accessory printer. A .csv file of selected sample data may be emailed,...

  • Page 12: General Screen Features

    • Sample Name and Sample Number: Tap the input box to enable a keyboard. A DeNovix approved barcode scanner may be used to enter sample names. • Sample Type and Factor Fields: Displays current sample type and associated factors used for concentration calculations.

  • Page 13: Report Screen

    General Screen Features Report Screen • Tap a record to highlight and select a record for export. More than one sample may be highlighted. • All highlighted sample records will be cleared from both the Report and Graph screens if the Delete icon is used. •...

  • Page 14: Graph Screen

    General Screen Features Graph Screen • Tap a record to highlight and display the sample absorbance spectrum on the graph. More than one sample spectrum may be added to the graph. • Tap a sample name and then tap the Edit icon to add or modify a sample name.

  • Page 15: Nucleic Acid Apps

    6. Nucleic Acid Apps dsDNA ssDNA Microarray 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. • Enter optional user-defined factor (ssDNA and Microarray) •...

  • Page 16: Dsdna

    Nucleic Acid dsDNA The dsDNA application is used to quantify samples based upon absorbance values at 260 nm. Screen Features • Sample Type: The sample type selection of dsDNA is preselected for this application. • Factor: The wavelength-dependent extinction coefficient factor of 50 is preselected for this application.

  • Page 17: Rna

    Nucleic Acid The RNA application is used to quantify samples based upon absorbance values at 260 nm. Screen Features • Sample Type: The sample type selection of RNA is preselected for this application. • Factor: The wavelength-dependent extinction coefficient factor of 40 is preselected for this application.

  • Page 18: Ssdna

    Nucleic Acid ssDNA The ssDNA application is used to quantify samples based upon absorbance values at 260 nm. Screen Features • Sample Type: The sample type selection of ssDNA is the default option for this application. • A Factor Input option is also available from the selector field. •...

  • Page 19: Microarray

    Nucleic Acid Microarray The Microarray application is used to quantify nucleic acid samples based upon absorbance 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 for this application.
  • Page 20 Nucleic Acid Baseline Correction The software anchors the visual spectrum display to the baseline at 750 nm for all measurements and automatically calculates a sloping baseline between 400 nm and 750 nm for dye concentration calculations. Dye List There are 12 preconfigured dye types in available for both the Microarray and Labeled Proteins applications.
  • Page 21 Nucleic Acid Preconfigured Dyes & Fluorophores Ext. Coeff A260 Factor A280 Factor 150000 0.08 0.08 250000 0.05 0.05 Cy5.5 250000 0.05 0.18 Alexa Fluor 405 34,000 0.23 Alexa Fluor 488 71,000 0.11 Alexa Fluor 555 150,000 0.08 0.08 Alexa Fluor 594 90,000 0.43 0.56...
  • Page 22 Nucleic Acid Nucleic Acid Concentration Calculations A modified Beer-Lambert equation is used to calculate concentrations as follows: c = (A * ε)/b c = the nucleic acid concentration in ng/microliter A = the absorbance in AU ε = the wavelength-dependent extinction coefficient in ng-cm/microliter. b= the pathlength in cm (10 mm) Sample type specific wavelength-dependent extinction coefficients : •...

  • Page 23: Protein Apps

    7. Protein Apps Protein A280 Labeled Proteins 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. • New protein types may be added to the selection list. •...

  • Page 24: Protein A280

    Protein Protein A280 The Protein A280 application is used to quantify samples based upon absorbance values at 280 nm. Screen Features • Sample Type: The sample type and associated mass extinction coefficients options include: Type E1% at 280 nm for 10 mm path. 1A=1mg/ml 6.67 13.7...
  • Page 25 Protein Baseline Correction Options • 340 nm -default selection • None • User Defined from 320 to 350 nm. Protein Type List New protein types may be added by selecting the Add New option from the sample type field on the Run screen. New protein types saved to the list are accessible for the Protein A280 and Labeled Proteins applications.

  • Page 26: Labeled Proteins

    Protein Labeled Proteins The Labeled Protein application is used to quantify protein samples based upon absorbance values at 280 nm as well as Dyes and Fluorophores at specific analysis wavelengths. Screen Features • Sample Type: The sample type and associated mass extinction coefficients options include: Type E1% at 280 nm for 10 mm path.
  • Page 27 Protein • Dye/Fluorophore Concentration Results: Concentration results are reported in units of μM. • A280*: The baseline and dye corrected 280 nm absorbance value. • AXXX: The baseline-corrected dye specific analysis wavelength absorbance value. Baseline Correction The software anchors the visual spectrum display to the baseline at 750 nm for all measurements and automatically calculates a sloping baseline between 400 nm and 750 nm for dye concentration calculations.
  • Page 28 The relationship between percent extinction coefficient (E1%) and molar extinction coefficient (Ext. Coeff) is: E1% = (Ext. Coeff *10) / molecular weight of protein The DeNovix software reports concentrations in mg/ml units in both the Protein A280 and Labeled Protein applications.

  • Page 29: Colorimetric Applications

    8. Colorimetric Applications with SmartFit Bradford Lowry Pierce 660 Refer to the manufacturer of the assay reagent for assay specific instructions. Quick Protocol 1. Launch the appropriate application from the Home screen. 2. Select the assay type on Run screen. 3.

  • Page 30: Standard Curve

    Colorimetrics Standard Curve 1. Use the drop-down feature to indicate that a new curve will be generated or to import a saved standard curve or standard curve concentration series. • When a previously saved curve is imported, a lock icon will appear. Tap the icon to unlock the curve data set to enable modifications and new absorbance measurements.
  • Page 31 Colorimetrics Saving a Standard Curve • Although generally not recommended, a standard curve may be saved and reused at a later date. Use the drop-down menu on the Standard Curve screen to select, add or edit a saved curve. Line Fit The average of the replicates is used to determine a best-fit trend line of the data set.

  • Page 32: Bca

    Colorimetrics The bicinchoninic acid assay (BCA assay) is used to quantify protein by measuring the Cu-BCA chelate formed in the presence of protein. • The reaction product is measured at 562 nm using a baseline correction at 750 nm. Results are reported in units of mg/ml. Bradford The Bradford assay is based upon a protein-induced absorbance shift of a Coomassie Blue dye as a method to determine protein concentration.

  • Page 33: Uv/Vis

    9. UV/Vis UV-Vis The UV/Vis module monitors up to 6 specific analysis wavelengths but does not calculate concentrations. Absorbance values for all wavelengths may be accessed via the export function. Quick Protocol 1. Launch the UV-Vis application from the Home screen. 2.
  • Page 34 UV/Vis Baseline Correction Options The SmartFit™ option baseline corrects the entire spectrum using the absorbance value of the wavelength with the lowest absorbance. • SmartFit™ -default selection • None • User Defined Baseline Correction Bichromatic normalizations correct for baseline offsets due to sample particulates or stray light artifacts.
  • Page 35 10. OD 600 OD 600 This application is generally used to determine the optical density of microbial cell cultures at 600 nm. Conversions to cells per ml are based upon a user defined factor. Quick Protocol 1. Launch the appropriate application from the Home screen. 2.
  • Page 36 1 * 10 cells. Baseline Correction Options • None -default • User Defined Baseline Correction As the microbial cell culture measurements are measurements of light scattering, bichromatic normalizations are not used as a default method by the DS-11 software.

  • Page 37: Kinetics

    The Kinetics application is a cuvette mode only application and is available for the DS-11 + model. The software Report Screen will display single or dual wavelength absorbance vs time data. The absorbance vs wavelength data may be viewed on the Graph screen.
  • Page 38 Kinetics Define Method Screen Features • Method Name: A method name is only required when saving the parameters to the Method List. • Heater: The heater may be set to temperatures between 30 to 45℃. The temperature box outline on the Run screen will turn from yellow to green when the set temperature is reached.
  • Page 39 Kinetics Run Screen Features • Method: All previously saved methods may be accessed using the Method selector drop-down list. • Heater Control: Tap the On/Off button to control the heater. The current temperature is displayed next to the control button. •...

  • Page 40: User Methods

    12. User Methods User Methods This application is used to create, save and access User Methods. Creating a New Method- Quick Protocol Launch the User Methods application from the Home screen. Use the drop-down menu on the Run screen to add a new method or select a previously saved method.

  • Page 41: Custom Formula Methods

    User Methods Primary Settings In addition to a method name, each new method requires a unique name and a specific set of parameters to be defined as described below. Custom Formula Methods • Analysis nm: Enter the primary wavelength of interest for the method. This wavelength will be used to determine which pathlength is utilized by the SmartPath™...
  • Page 42 User Methods Formula Guidelines • Use the A(x) button on the input screen to specify the absorbance value of a specific wavelength. Enter the wavelength within the parenthesis. Example: A(260) • • Check that closed sets of parenthesis are included when entering complex formulas.

  • Page 43: Standard Curve Methods

    User Methods Standard Curve Methods • Units: Enter custom units. The units are used as the results field label. • Analysis nm: Enter the wavelength for which the absorbance value is used to calculate sample concentrations. The Analysis nm is also used to determine which pathlength is utilized by the SmartPath™...
  • Page 44 User Methods Additional Settings The available additional settings for both method types include: • Mode: The default option is Microvolume for the Fixed Wavelengths and Standard Curve methods and Cuvette 10 nm for Kinetics methods. • Baseline Correction: The default value is 840 nm. •...

  • Page 45: Screen Capture And Export

    Screen Capture • The DS-11 software supports the screen capture of most screens as .jpg images. • The files may be emailed, saved to a USB device or printed to a DeNovix product compatible accessory printer. Export Selected • The data associated with highlighted samples on a Report or Graph screen may be exported via email or saved to a USB device as .csv files.
  • Page 46 Printer • Screen captures as well as selected sample data and graphs may be printed using a DeNovix product compatible accessory printer. • Screen shots and data results are formatted to fit on a 4 x 6 label. All images and tables are printed in black and white.

  • Page 47: Utility Apps

    14. Utility Apps Accounts Database Settings Updater Accounts User accounts are used as a means of managing default settings within specific apps as well as a means of segregating data within the database. System Accounts The software comes with two system accounts which may not be deleted or modified.
  • Page 48 If an account is deleted, all associated methods are still available for general use. Contact the holder of an administrator account if a user account password is forgotten. Contact DeNovix customer support or your local distributor if the Primary Administrator password is forgotten.

  • Page 49: Data

    Utility Apps Data This app allows the user to search for past data using either a Quick Search or an Advanced Search mode. The data of interest is then available for review on a Report Screen and a Graph screen. The data is available for export or printing. •...

  • Page 50: Settings

    About Updater This app is found on page 2 of DeNovix home screen and is used to update the software. 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...

  • Page 51: Updater

    Utility Apps Updater This app is found on page 2 of DeNovix home screen and is used to update the software. 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 the website onto a thumb drive.

  • Page 52: Lab Tool Apps

    15. Lab Tool Apps Calculators Timer Calculators 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. •...

  • Page 53: Timer

    Lab Tools 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. •...

  • Page 54: Maintenance

    16. Maintenance Cleaning 1.Pipette 3-4 μL of dH20 onto the bottom sample surface. Lower the upper arm. Wait 2-3 minutes. 2. Wipe away the water from both the upper and lower sample surfaces with a dry, lint-free lab wipe. Do not use a spray bottle to apply water or any other General General General...
  • Page 55 Exception: Do not use Hydrofluoric Acid (HF) as the fluoride ion will dissolve the quartz fiber optic cables. Cuvette Calibration Check A specific cuvette calibration check procedure is not built into the DeNovix DS-11+ software. Customer Support Contact DeNovix Customer Support at 1-302.442.6911 or info@denovix.com...

  • Page 56: Troubleshooting And Diagnostics

    17. Troubleshooting and Diagnostics Diagnostics 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: • Ensure microvolume measurement surfaces are clean prior to making the Blank measurement.

  • Page 57: Software

    Please visit the Product Accessories page at www.denovix.com for a list of the approved models. For accessory product troubleshooting and warranty information, please contact the manufacturer of the product. DeNovix support is limited to the specific use of the product with the DS-11 instrument.

  • Page 58: Self Check

    • Ensure that both the upper and lower microvolume measurement surfaces are clean prior to starting the Self Check assessment. • For DS-11+ models, remove any cuvettes from the holder block and ensure the light path is clear of all obstructions.

  • Page 59: Microvolume Pathlength Verification

    Troubleshooting & Diagnostics Microvolume Pathlength Verification The DeNovix LC-NA and HC-NA are low and high concentration solutions of aqueous nicotinic acid. These solutions are used to verify that the microvolume pathlengths are within specifications. The use of two solutions ensures that an optimal target absorbance signal is available for all pathlengths when verifying calibration.
  • Page 60 • Note: Only the LC-NA and HC-NA standards 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 check procedure.

  • Page 61: Verification Check Troubleshooting

    Troubleshooting & Diagnostics Verification Check Troubleshooting Dirty measurement surfaces or improper blank. Clean the surfaces, measure a new Blank using fresh source of dH20 and Low Absorbance Low Absorbance Low Absorbance Low Absorbance restart the procedure using a new vial of XXX. Values Values Values...

  • Page 62: Customer Support

    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 no responsibility and will not be liable for any errors, omissions, damage or loss that...

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