White FR-2000C User Manual

NanoDrop 2000/2000c Spectrophotometer V1.0 User Manual

Section 2-Software 2. Software Computer Requirements • Microsoft Windows XP or Vista (32 bit) operating system • 1.5GHz or higher processor • CD

Section 2-Software Cable Connections To make measurements with the instrument, connect the USB cable to the instrument and the PC, plug in the 12V po

Section 2-Software • Dye/ Chrom. Editor (Micro Array and Protein & Labels only) - enables the user to enter and edit new dyes in addition to pred

Section 2-Software - E-mail current workbook - automatically attaches the current workbook to a new email message. When sending data to NanoDrop prod

Section 2-Software Right Pane The right pane displays the main menu which includes the following: • Group drop-down box - selects the preferred ma

Section 2-Software • Sample labels (UV-Vis only) - selects whether absorbance values for specific wavelengths are displayed on the graph for the most

Section 2-Software Data and Account Management My Data Sample measurement data is recorded in workbooks that can be filed in a user-specified locat

Section 2-Software - Report, Excel XML Spreadsheet (*.xml) - saves a report in a format which can be opened in Excel. Only the columns displayed in t

Section 2-Software Reprocess The Reprocess feature is available in the top left pane of the reports page for some applications. This feature recalcul

Section 2-Software • Report Master Page - defines the layout and appearance of headers and footers for printed pages. Using this tab, parameters such

The information in this publication is provided for reference only. All information contained in this publication is believed to be correct and comple

Section 2-Software The left side of the Accounts page displays a list of access control categories. Each of these categories includes softwar

Section 2-Software Drop downs and list boxes: • List names from - displays a list of available domains from which to choose. • Organization - disp

Section 3- Applications 3. Applications Overview UV-VIS spectrophotometry is easy for micro-volume samples using NanoDrop 2000/2000c spectrophotome

Section 3- Applications A Quick Start Guide that includes a blanking procedure can be accessed from “Appendices” of the NanoDrop 2000 User Manual PD

Section 3- Applications Nucleic Acid Overview Nucleic acid samples can be easily checked for concentration and quality using the NanoDrop 2000/2000

Section 3- Applications Unique Screen Features The right pane displays features specific to the Nucleic Acid application. Task bars in the left pane

Section 3- Applications • 260/230 - ratio of absorbance at 260 nm and 230 nm. This is a secondary measure of nucleic acid purity. The 260/230 values

Section 3- Applications After the measurement: - Simply wipe the upper and lower pedestals using a dry laboratory wipe and the instrument is ready

Section 3- Applications To calculate the melting point of a DNA sequence: 1. Enter the base sequence as described above. If a base sequence has al

Section 3- Applications Micro Array Overview The capability to pre-select viable fluorescently-tagged hybridization probes for use on micro arrays

Table of Contents 1. INTRODUCTION...

Section 3- Applications The spectral display shows data for the current sample normalized to a 1 mm path if measured using the pedestal mode or the p

Section 3- Applications 4. Use the drop-down lists in the Dye 1 or Dye 2 box to select the appropriate dye (or dyes). The default for Dye 1 is Cy3 a

Section 3- Applications To use the Oligo Calc: 1. Use one of the following options to enter in a base sequence: - The buttons below the Base Seq

Section 3- Applications Melting Point analysis result fields include: • Salt-Adjusted - calculates the melting point of the base sequence without a

Section 3- Applications UV-Vis Overview The UV-Vis application allows the NanoDrop 2000/2000c to function as a conventional spectrophotometer. Samp

Section 3- Applications - The shorter pathlength is advantageous for highly concentrated samples. Although this is an automatic function in other a

Section 3- Applications recommended that cuvettes be removed from the instrument prior to making a pedestal measurement to ensure that the pedestal a

Section 3- Applications Protein A280 Overview Proteins, unlike nucleic acids, can exhibit considerable diversity. The Protein A280 application is a

Section 3- Applications Unique Screen Features The right pane displays features specific to the Protein A280 application. Task bars in the left pane

Section 3- Applications • Ext. Coeff, E1% L/gm-cm - appears when Other Protein (E1%) is selected. The appropriate extinction coefficient should be e

Unique Screen Features ...

Section 3- Applications 8. Enter a sample ID in the appropriate field, load the first sample as described for the blank above and click Measure.

Section 3- Applications Proteins & Labels Overview The Proteins & Labels application can be used to determine protein concentration (A280

Section 3- Applications Unique Screen Features The right pane displays features specific to the Protein & Labels application. Task bars in the l

Section 3- Applications - uM - is the concentration based upon the respective dye’s extinction coefficient. Concentration units may be selected from

Section 3- Applications - Cuvette Option (Model 2000c only): Insert the cuvette noting the direction of the light path indicated by the etched arrow

Section 3- Applications Protein BCA Overview The BCA (Bicinchoninic Acid) assay is a colorimetric method for determining the total protein concentr

Section 3- Applications Pedestal Reconditioning Solutions and reagents containing surfactants may “un-condition” the measurement pedestal surfaces

Section 3- Applications • Standards radio button - enables entry of standard names and concentrations into the standards table when selected. • Co

Section 3- Applications Note: If selecting a previously saved workbook, all concentration calculations for newly measured samples will be based upo

Section 3- Applications Note: A fresh aliquot of sample should be used for each measurement. After the measurement: - Simply wipe the upper a

Section 1-Introduction 1. Introduction Instrument Description Thermo Scientific NanoDrop™ 2000/2000c Spectrophotometers measure 0.5- 2 ul samples wi

Section 3- Applications Protein Lowry Overview The Lowry assay is an alternative method for determining protein concentration based on the widely u

Section 3- Applications Unique Screen Features The right pane displays features specific to the Protein Lowry application. Task bars in the left pan

Section 3- Applications Lowry Standard Curves A standard curve is required for Lowry assays. Example Standard Curve: 5:1 reagent/sample volume.

Section 3- Applications Making Lowry Assay Measurements • Refer to the manufacturers’ guidelines and recommendations for sample preparation. • T

Section 3- Applications After the measurement: - Simply wipe the upper and lower pedestals using a dry laboratory wipe and the instrument is ready

Section 3- Applications Protein Bradford Overview The Bradford Assay is a commonly used method for determining protein concentration. It is often u

Section 3- Applications When using the cuvette option, it is essential that sufficient sample volume be used to ensure that the light path is passing

Section 3- Applications • Samples radio button – Once the criteria have been met for a valid curve, the Sample ID field will become active when se

Section 3- Applications • In order to establish a new standard curve, a new workbook must be created. Colorimetric applications will offer several

Section 3- Applications 7. After all of the Standards have been measured, click on the Samples radio button. Enter a sample ID. Load 2 µL of sample

Section 1-Introduction Sample Retention Pedestal Measurements A 1 - 2 µL sample is pipetted onto a measurement pedestal. A smaller, 0.5 µL volume sam

Section 3- Applications Protein Pierce 660 nm Overview The Thermo Scientific Protein Pierce 660 nm assay reagent is a ready-to-use formulation tha

Section 3- Applications Unique Screen Features The right pane displays features specific to the Protein Pierce 660 nm application. Task bars in the

Section 3- Applications Protein Pierce 660 nm Assay Workbooks When the Protein Pierce 660 nm application is selected from the main menu, the follow

Section 3- Applications Note: This is unlike the other colorimetric assays on the NanoDrop 2000/2000c where it is recommended that water be used a

Section 3- Applications - Select the file drop-down option Use current settings as default as a convenient way to limit set-up time for each new wor

Section 3- Applications Cell Cultures Overview Using an absorbance spectrophotometer to monitor light scattered by non-absorbing suspended cells is

Section 3- Applications Unique Screen Features The right pane displays features specific to the Cell Cultures application. Task bars in the left pan

Section 3- Applications 4. Establish a blank using the appropriate buffer. The reference or blank solution generally is the buffer that the molecule

Section 3- Applications Application FAQs Q: Does the NanoDrop 2000/2000c produce results for a continuous spectrum or just selected wavelength

Section 3- Applications Q: I am using a colorimetric method (e.g. Bradford, BCA etc.,) to determine the protein concentration. Can I measure the samp

Section 1-Introduction Cuvette Measurements The NanoDrop 2000c will accept 10 mm cuvettes up to 48 mm tall. When measuring samples using micro, semi

Section 4- Method Editor 4. Method Editor The Method Editor application and the List of Custom Methods box on the main menu are used to create, edit,

Section 4- Method Editor Left Pane When the Method Editor task bar is selected, the following icons will appear at the top of the left pane: • New

Section 4- Method Editor • Additional Measurements - adds user-selected or user-defined formulas for additional processing of data. Refer to “Creati

Section 4- Method Editor Example: Lysozyme (A(280)* 10 / 26.4) / Path() mg/ml The above example will result in a “Lysoz

Section 4- Method Editor Sharing of Custom Methods Custom methods may be shared by simply pasting a copy of the desired method into the appropriate f

Section 5-Kinetics 5. Kinetics The NanoDrop 2000c can be used to make time-based kinetic measurements. The Kinetics Editor is used to create, edit, s

Section 5-Kinetics Right Pane When Kinetics Editor is selected, clicking on the icon at the top left will start a new method. A two-step wizard styl

Section 5-Kinetics Data Acquisition Page There are two graphical displays in the right pane of the Kinetics screen: • The Wavelength table to th

Section 5-Kinetics Note: Rate vectors are by default locked to the curve and will display the best fit for the two time points selected. Highlight

Section 5-Kinetics - It may take between 1- 10 minutes for the cuvette holder to reach temperature. - The heater will stop heating when another, wo

Section 1-Introduction Blanking and Absorbance Calculations When a NanoDrop 2000/2000c spectrophotometer is blanked, a spectrum is taken of the refer

Section 6- Warranty and Maintenance 6. Warranty and Maintenance Warranty All NanoDrop spectrophotometers and accessories manufactured by Thermo Fish

Section 6- Warranty and Maintenance Maintenance of the Sample Retention System Cleaning The primary maintenance requirement for the NanoDrop 2000/2

Section 6- Warranty and Maintenance Pedestal Reconditioning The Bradford reagent as well as other buffers containing surfactants may “un-condition” t

Section 6- Warranty and Maintenance Solvent Compatibility The NanoDrop 2000/2000c Spectrophotometer pedestals are compatible with most solvents typic

Section 6- Warranty and Maintenance Maintenance FAQs Q. How do I clean the pedestal? A: Add 2-3 µL of water to the bottom pedestal surface and lower

Section 7- Diagnostics and Troubleshooting 7. Diagnostics and Troubleshooting The Diagnostics task bar accesses both the Intensity Check and the Cali

Section 7- Diagnostics and Troubleshooting Calibration Check It is recommended that a pedestal calibration check be performed every six months to ver

Section 7- Diagnostics and Troubleshooting 7. Follow the on-screen prompts in the Customer Guidance text box. Using individual 1µL aliquots of the CF

Section 7- Diagnostics and Troubleshooting 1. Exit the software. 2. Disconnect the instrument power cord and USB cable. 3. Reconnect the instrum

Section 7- Diagnostics and Troubleshooting If the warning persists and the user visually confirms that the liquid column is forming, perform a calibra

Section 1-Introduction Fluorescent Dyes The software uses the general form of the Beer-Lambert equation to calculate fluorescent dye concentrations

Section 7- Diagnostics and Troubleshooting Note: Do not use a squirt or spray bottle to apply de-ionized water. • Use a 1.5-2 µL sample volume. Un

Section 7- Diagnostics and Troubleshooting • Wavelength accuracy of the spectrophotometers Although the absorbance of a nucleic acid at 260nm is gene

Section 7- Diagnostics and Troubleshooting In addition, application screen captures and Intensity Check .JPGs are of great use in diagnosing problems.

Section 7- Diagnostics and Troubleshooting Troubleshooting FAQs Q: Why do I have negative absorbance values? A: A blank measurement was made either u

Section 8-Appendices 8. Appendices Quick Start Guide The Quick Start Guide includes information about a recommended blanking procedure to ensure pr

INSTRUCTIONS NanoDrop2000/2000c Thermo Fisher Scientific - NanoDrop products Wilmi

Thermo Fisher Scientific - NanoDrop products Wilmington, Delaware USA

Rev 3/09 T031‐ TECHNICAL BULLETINNanoDrop2000/2000c Thermo Fisher Scientific - NanoDrop products Wilmington, D