Page 1 NanoDrop Micro-UV/Vis Spectrophotometer NanoDrop Eight User Guide M020 NanoDrop Eight UG Revision Date April 2023...
Page 2 © 2023 Thermo Fisher Scientific Inc. All rights reserved. For U.S. Technical Support, please contact: For International Support, please contact: http://www.thermofisher.com/ Thermo Fisher Scientific NanoDropSupport 3411 Silverside Road Tatnall Building, Suite 100 Contact your local distributor. For contact Wilmington, DE 19810 U.S.A. information go to: Telephone: 302 479 7707 http://www.thermofisher.com/...
Page 3: Table Of Contents
Settings for Microarray Measurements ......31 Calculations for Microarray Measurements.....35 Thermo Scientific NanoDrop Eight User Guide...
Page 4 Protein Bradford Reported Results ......98 Settings for Protein Bradford Measurements ....100 NanoDrop Eight User Guide Thermo Scientific...
Page 5 Run a Blanking Cycle ........162 Thermo Scientific NanoDrop Eight User Guide...
Page 6 Basic Instrument Operations ....... .164 NanoDrop Eight Home Screen......164 NanoDrop Eight Measurement Screens .
Page 7: Chapter 1 About The Spectrophotometer
1 µl samples in one measurement cycle. The software allows the user to measure samples using either the full 8-channel mode or a convenient single sample mode. The NanoDrop Eight software is installed on a local PC used to control the instrument and view data.
Page 8: Features
Features TheNanoDrop Eight spectrophotometer features the patented micro-volume sample retention system. USB-B port Connect the NanoDrop Eight to your PC via USB to operate the instrument using the PC software. NanoDrop Eight User Guide Thermo Scientific...
Page 9: Accessories
About the Spectrophotometer Accessories Accessories This section lists the accessories included for use with the NanoDrop Eight. PR-1 Pedestal Reconditioning Kit Specially formulated conditioning compound that can be applied to the pedestals to restore them to a hydrophobic state (required to achieve adequate surface tension for accurate sample measurements).
Page 10: Instrument Detection Limits
About the Spectrophotometer Instrument Detection Limits Instrument Detection Limits Upper Detection Limit Pathlength (mm) (10 mm Equivalent Absorbance) 12.5 NanoDrop Eight User Guide Thermo Scientific...
Page 11: Chapter 2 Instrument Set Up
Register Your Instrument Register your instrument to receive e-mail updates on software and accessories for the NanoDrop Eight instrument. An Internet connection is required for registration. To register your instrument From any PC that is connected to the Internet, use any web browser to navigate to www.thermofisher.com/nanodropsw.
Page 12: Update Software
Update Software Update Software Quickly and easily download and install the latest NanoDrop Eight software and release notes from our website. Follow the steps to update or upgrade the NanoDrop Eight software on a personal computer (PC). An Internet connection is required to download software.
Page 13: Chapter 3 Application Measurement Ranges
2.0 and 100 ng/µL samples; ±2% for samples >100 ng/µL DNA Microarray 1.3 ng/µL 495 ng/µL ±2.0 ng/µL for sample concentrations (ssDNA) between 2.0 and 100 ng/µL samples; ±2% for samples >100 ng/µL Thermo Scientific NanoDrop Eight User Guide...
Page 14 ±3 µg/mL for 50–125 µg/mL samples reagent/sample ±2% for samples > 125 µg/mL volume) ±3 µg/mL for 25–125 µg/mL samples 1000 µg/mL 25 µg/mL (7.5:1 ±2% for samples >125 µg/mL reagent/sample volume) Based on five replicates (SD=ng/µL; CV=%) NanoDrop Eight User Guide Thermo Scientific...
Page 15: Detection Limits For Pre-Defined Dyes
±2% for samples >8.0 pmol/µL Alexa Fluor 546 0.3 pmol/µL 145 pmol/µL ±0.30 pmol/µL for sample concentrations between 0.30 and 6.0 pmol/µL; ±2% for samples >6.0 pmol/µL Values are approximate Based on five replicates (SD=ng/µL; CV=%) Thermo Scientific NanoDrop Eight User Guide...
Page 16 Application Measurement Ranges This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 17: Chapter 4 Nucleic Acid Applications
• Do not use a squirt or spray bottle on or near the instrument as liquids will flow into the instrument and may cause permanent damage. • Do not use hydrofluoric acid (HF) on the pedestals. Fluoride ions will permanently damage the quartz fiber optic cables. Thermo Scientific NanoDrop Eight User Guide...
Page 18 Measure dsDNA, ssDNA or RNA Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 19: Best Practices For Nucleic Acid Measurements
• Isolate and purify nucleic acid samples before measurement to remove impurities. Depending on the sample, impurities could include DNA, RNA, free nucleotides, proteins, some buffer components and dyes. See Preparing Samples for more information. Thermo Scientific NanoDrop Eight User Guide...
Page 20: Related Topics
Use a 1-2 µL sample volume. See Recommended Sample Volumes for more information. Related Topics • Measure a Micro-Volume Sample • Best Practices for Micro-Volume Measurements • Prepare Samples and Blanks • Basic Instrument Operations NanoDrop Eight User Guide Thermo Scientific...
Page 21: Nucleic Acid Reported Results
Well plate Nucleic acid Purity ratios Click row to select sample options concentration and update spectrum. Note Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. Thermo Scientific NanoDrop Eight User Guide...
Page 22: Settings For Nucleic Acid Measurements
As a result, absorbance of sample spectrum is zero at specified baseline correction wavelength. NanoDrop Eight User Guide Thermo Scientific...
Page 23: Calculations For Nucleic Acid Measurements
• ssDNA (factor = 33 ng-cm/µL) concentration. For the Custom Factor application, the user-specified factor is • RNA (factor = 40 ng-cm/µL) used. • Custom Factor (user entered factor between 15 ng-cm/µL and 150 ng-cm/µL Thermo Scientific NanoDrop Eight User Guide...
Page 24 • For micro-volume measurements, the software selects the optimal pathlength (between 1.0 mm and 0.1 mm) based on sample absorbance at the analysis wavelength. • Displayed spectra and absorbance values are normalized to a 10 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 25 • Monitor wavelength - Enter an additional wavelength whose absorbance value you want included in the report. • Corrected - Displays the corrected analyte concentration determined using the Acclaro software, if one is available. Thermo Scientific NanoDrop Eight User Guide...
Page 26 Nucleic Acid Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 27: Measure Microarray
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 28 When the sample measurement is completed, the spectrum and reported values are displayed (see the next section). 8. When you are finished measuring samples, select End Experiment. 9. Lift the arm and clean all pedestals with a new wipe. NanoDrop Eight User Guide Thermo Scientific...
Page 29 Typical microarray spectrum Related Topics • Best Practices for Nucleic Acid Measurements • Measure a Micro-Volume Sample • Best Practices for Micro-Volume Measurements • Prepare Samples and Blanks • Basic Instrument Operations Thermo Scientific NanoDrop Eight User Guide...
Page 30: Microarray Reported Results
• Analysis correction is performed at 340 nm (absorbance value at 340 nm is subtracted from absorbance values at all wavelengths in sample spectrum). • Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 31: Settings For Microarray Measurements
When selected, available DNA base units (i.e., G, A, T, C) appear as keys. Define sequence by selecting appropriate keys. Factor is calculated automatically based on widely accepted value for each base unit. Thermo Scientific NanoDrop Eight User Guide...
Page 32: Dye/Chromophore Editor
Use the Dye/Chromophore Editor to add a custom dye to the list of available dyes in Microarray Setup Proteins & Labels Setup. You can also specify which dyes are available in that list. To access the Dye/Chromophore Editor, from the Home screen, select Settings > Dye Editor. NanoDrop Eight User Guide Thermo Scientific...
Page 33 L/mole-cm (typically provided by dye manufacturer) – specify Wavelength in nm (between 350 nm and 840 nm) that will be used to measure dye’s absorbance – specify dye’s correction values at 260 nm and 280 nm – select Save Thermo Scientific NanoDrop Eight User Guide...
Page 34 Delete custom dye Tip Dyes pre-defined in the software cannot be deleted. – select custom dye – click NOTICE Deleting a custom dye permanently removes the dye and all associated information from the software. NanoDrop Eight User Guide Thermo Scientific...
Page 35: Calculations For Microarray Measurements
Note: See Sample Type for more information. Tip: Ideally, the factor or extinction coefficient should be determined empirically using a solution of the study nucleic acid at a known concentration using the same buffer. Thermo Scientific NanoDrop Eight User Guide...
Page 36 • The final corrected absorbance at 260 nm is reported and used to calculate sample concentration. A280 absorbance • Analysis-corrected and normalized absorbance value at 280 nm (minus the A280 dye correction) is used to calculate an A260/A280 ratio. NanoDrop Eight User Guide Thermo Scientific...
Page 37 • For micro-volume measurements, the software selects the optimal pathlength (between 1.0 mm and 0.1 mm) based on sample absorbance at the analysis wavelength. • Displayed spectra and absorbance values are normalized to a 10 mm pathlength equivalent. Thermo Scientific NanoDrop Eight User Guide...
Page 38 Note: Although purity ratios are important indicators of sample quality, the best indicator of DNA or RNA quality is functionality in the downstream application of interest (e.g., microarray). Related Topics • Calculations for Nucleic Acid Measurements NanoDrop Eight User Guide Thermo Scientific...
Page 39: Measure Using A Custom Factor
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 40 When the sample measurement is completed, the spectrum and reported values are displayed (see the next section). 8. When you are finished measuring samples, select End Experiment. 9. Lift the arm and clean all pedestals with a new wipe. Typical nucleic acid spectrum NanoDrop Eight User Guide Thermo Scientific...
Page 41: Custom Factor Reported Results
Tips: Click sample row to select sample and update spectrum Shift-click multiple sample rows to overlay spectra Click a sample and hover locations on spectra to view measurement values Thermo Scientific NanoDrop Eight User Guide...
Page 42: Settings For Nucleic Acid Measurements Using A Custom Factor
= molar extinction coefficient at 260 nm in ng-cm/µL sample pathlength in cm (1 cm for nucleic acids measured with the NanoDrop Eight instruments) Baseline Correction On or off Optional user-defined baseline correction. Can be used to correct for any offset caused by light scattering...
Page 43: Detection Limits For Nucleic Acid Measurements Using A Custom
For example, for a sample measurement using an extinction coefficient of 31, the equation looks like this: (200 AU * 31 ng-cm/µL) = 6,200 ng/µL Related Topics • Detection Limits for All Applications Thermo Scientific NanoDrop Eight User Guide...
Page 44 Nucleic Acid Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 45: Measure Oligo Dna Or Oligo Rna
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 46 8. When you are finished measuring samples, tap End Experiment 9. Lift the arm and clean all pedestals with a new wipe. Example Oligo DNA spectrum Related Topics • Best Practices for Nucleic Acid Measurements NanoDrop Eight User Guide Thermo Scientific...
Page 47: Oligo Reported Results
Click row to select sample and update spectrum; click more rows to overlay spectra Wellplate view; Well plate Purity ratios toggle to view/ options hide well plate Sample name; Nucleic acid Select to edit concentration Thermo Scientific NanoDrop Eight User Guide...
Page 48 • oligo sequence • baseline correction Note The five nucleotides that comprise DNA and RNA exhibit widely varying A260/A280 ratios. See Oligo Purity Ratios for more information. Related Topics • Basic Instrument Operations • Oligo Calculations NanoDrop Eight User Guide Thermo Scientific...
Page 49: Settings For Oligo Dna And Oligo Rna Measurements
 f = 1/( * b) where:  f= factor = molar extinction coefficient at 260 nm in ng-cm/µL sample pathlength in cm (1 cm for nucleic acids measured with the NanoDrop Eight instrument) Thermo Scientific NanoDrop Eight User Guide...
Page 50: Detection Limits For Oligo Dna And Oligo Rna Measurements
To calculate upper detection limits in ng/µL, use the following equation: (upper absorbance limit * extinction coefficient instrumen sample For example, for a sample measurement using an extinction coefficient of 55, the equation looks like this: (200 AU * 55 ng-cm/µL) = 11,000 ng/µL NanoDrop Eight User Guide Thermo Scientific...
Page 51: Calculations For Oligo Dna And Oligo Rna Measurements
Tip: The extinction coefficient is wavelength specific for each oligonucleotide and can be affected by buffer type, ionic strength and pH. Thermo Scientific NanoDrop Eight User Guide...
Page 52 • For micro-volume measurements, the software selects the optimal pathlength (between 1.0 mm and 0.1 mm) based on sample absorbance at the analysis wavelength. • Displayed spectra and absorbance values are normalized to a 10 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 53 See side bar for more information. Related Topics • Calculations for Nucleic Acid Measurements Thermo Scientific NanoDrop Eight User Guide...
Page 54 Nucleic Acid Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 55: Chapter 5 Protein Applications
• Do not use a squirt or spray bottle on or near the instrument as liquids will flow into the instrument and may cause permanent damage. • Do not use hydrofluoric acid (HF) on the pedestals. Fluoride ions will permanently damage the quartz fiber optic cables. Thermo Scientific NanoDrop Eight User Guide...
Page 56 Measure Protein A280 Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 57: Best Practices For Protein Measurements
Note Extraction reagents that contribute absorbance between 200 nm and 280 nm will affect measurement results if present in samples (even residual amounts). • Ensure the sample absorbance is within the instrument’s absorbance detection limits. Thermo Scientific NanoDrop Eight User Guide...
Page 58 Use a 2 µL sample volume. See Recommended Sample Volumes for more information. Related Topics • Best practices for protein measurements • Measure a Micro-Volume Sample • Prepare Samples and Blanks • Basic Instrument Operations NanoDrop Eight User Guide Thermo Scientific...
Page 59: Protein A280 Reported Results
Note Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. Protein A280 reported values • Protein concentration • Absorbance at 280 nm • Purity ratio • Sample type • Baseline correction wavelength Thermo Scientific NanoDrop Eight User Guide...
Page 60: Settings For Protein A280 Measurements
If you only need a rough estimate of protein concentration and the sample extinction coefficient is unknown, select the 1 Abs=1 mg/mL sample type option. NanoDrop Eight User Guide Thermo Scientific...
Page 61 ( ) of 26.4 L/gm-cm at 280 nm for 1% (i.e., 10 mg/mL) lysozyme solution. Assumes molar extinction coefficient for egg white lysozyme ranges between 36,000 M and 39,000 M Thermo Scientific NanoDrop Eight User Guide...
Page 62 As a result, absorbance of sample spectrum is (340 nm) zero at specified baseline correction wavelength. Tip: If the sample has a modification that absorbs light at 340 nm, select a different correction wavelength or turn off Baseline Correction. NanoDrop Eight User Guide Thermo Scientific...
Page 63: Protein Editor
4. Specify whether to enter Molar Extinction coefficient or Mass Extinction coefficient for custom protein. – If Mass Extinction coefficient is selected, enter mass extinction  coefficient in L/gm-cm for 10 mg/mL ( 1%) protein solution. Thermo Scientific NanoDrop Eight User Guide...
Page 64 4. Click OK Delete custom protein 1. In Protein Editor, click to select a custom protein to delete 2. click Note Deleting a custom protein permanently removes the protein and all associated information from the software. NanoDrop Eight User Guide Thermo Scientific...
Page 65: Detection Limits For Protein A280 Measurements
Note: Dividing the measured absorbance of a sample solution by its molar extinction coefficient yields the molar concentration of the sample. See Published Extinction Coefficients for more information regarding molar vs. mass concentration values. Thermo Scientific NanoDrop Eight User Guide...
Page 66 • Other protein ( 1%), user-specified mass ext. solution of the study protein at a known coefficient concentration using the same buffer. • Note: See Sample Type for details. NanoDrop Eight User Guide Thermo Scientific...
Page 67 = (A / 1%) * 10 a conversion factor of 10. protein Tip: The NanoDrop Eight software Example: If measured absorbance for a protein sample at includes the conversion factor when 280 nm relative to the reference is 5.8 A, protein reporting protein concentrations.
Page 68 (e.g., real-time PCR). • Contaminant - Displays contaminant identified by the Acclaro software, if one is available. • Corrected - Display the corrected analyte concentration determined using the Acclaro software, if one is available. NanoDrop Eight User Guide Thermo Scientific...
Page 69: Measure Protein A205
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 70 9. Lift the arm and clean all pedestals with a new wipe. Related Topics • Best Practices for Protein Measurements • Measure a Micro-Volume Sample • Prepare Samples and Blanks • Basic Instrument Operations NanoDrop Eight User Guide Thermo Scientific...
Page 71: Protein A205 Reported Results
280 nm Protein concentration Absorbance at 205 nm Protein A205 reported values • Protein concentration • Absorbance at 205 nm • Absorbance at 280 nm • Sample type • Baseline correction Thermo Scientific NanoDrop Eight User Guide...
Page 72: Settings For Protein A205 Measurements
Tip: If the sample has a modification that absorbs light at 340 nm, select a different correction wavelength or turn off Baseline Correction. Related Topics • Instrument Settings NanoDrop Eight User Guide Thermo Scientific...
Page 73: Calculations For Protein A205 Measurements
205 nm is reported and used to calculate protein concentration. A280 absorbance • Normalized and baseline-corrected (if selected) absorbance value at 280 nm is also reported. Thermo Scientific NanoDrop Eight User Guide...
Page 74 10 mm pathlength equivalent. Reported Values • Protein concentration. Reported in selected unit (mg/mL or µg/mL). Calculations are based on Beer-Lambert equation using corrected protein absorbance value. Related Topics • Beer-Lambert Equation • Protein A280 Calculations NanoDrop Eight User Guide Thermo Scientific...
Page 75: Measure Proteins And Labels
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 76 9. Lift the arm and clean all pedestals with a new wipe. Peptide backbone A280 absorbance peak used to calculate protein concentration Dye absorbance peak used to calculate dye concentration Typical sample spectrum measured with Proteins & Labels NanoDrop Eight User Guide Thermo Scientific...
Page 77: Proteins & Labels Reported Results
UV spectrum options Analysis Correction Menu of table options; click to choose which columns to report Click row to select sample and update spectrum. Sloping Dye Sample name; Protein Correction select to edit concentration concentration(s) Thermo Scientific NanoDrop Eight User Guide...
Page 78: Settings For Proteins And Labels Measurements
• Basic Instrument Operations • Proteins & Labels calculations Settings for Proteins and Labels Measurements To show the Proteins & Labels settings, from the Proteins & Labels measurement screen, select Proteins & Labels Setup. NanoDrop Eight User Guide Thermo Scientific...
Page 79 555, 594, 647, or 660 Editor for specific Dye/Chrom. Editor. values for each Dye 1/Dye 2 picomoles/microliter not applicable Select unit for reporting dye concentrations. Unit (pmol/µl), micromoles (uM), or millimoles (mM) Thermo Scientific NanoDrop Eight User Guide...
Page 80: Detection Limits For Proteins And Labels Measurements
For example, if the sample’s mass extinction coefficient at 280 nm is 6.7 for a 1% (10 mg/mL) solution, the equation looks like this: (200 / 6.7) * 10 = 298.5 (or ~300) Related Topics • Detection Limits for All Applications NanoDrop Eight User Guide Thermo Scientific...
Page 81: Calculations For Proteins And Labels Measurements
280 nm is reported and used to calculate protein concentration. • If a Dye is used, the normalized, analysis-corrected and dye-corrected absorbance value at 280 nm is reported and used to calculate protein concentration. Thermo Scientific NanoDrop Eight User Guide...
Page 82 Beer-Lambert equation using corrected protein absorbance value. • Dye1/Dye2 concentration. Reported in pmol/µL. Calculations are based on Beer’s Law equation using (sloping) baseline-corrected dye absorbance value(s). Related Topics • Beer-Lambert Equation • Protein A280 Calculations NanoDrop Eight User Guide Thermo Scientific...
Page 83: Measure Protein Bca
Protein assay kits and protocols Please refer to the NanoDrop website for up-to-date kits and protocols for the NanoDrop Eight instrument. Follow the assay kit manufacturer’s recommendations for all standards and samples (unknowns). Ensure each is subjected to the same timing and temperature throughout the assay.
Page 84 Measure Protein BCA Protein standards for generating a standard curve may also be provided by the kit manufacturer. Since the NanoDrop Eight pedestals can measure higher protein concentrations than traditional cuvette-based spectrophotometers, you may need to supply your own protein standards at higher concentrations than provided by the manufacturer.
Page 85 O (deionized water). For Protein Pierce 660, blank with the reference solution. • Measure the reference and all standards before you start analyzing samples. (After the first sample has been measured, no additional changes are allowed to the standard curve.) Thermo Scientific NanoDrop Eight User Guide...
Page 86 (1.0 is a perfect fit; all points lie exactly on the curve). Standards are listed in the lower half of the screen in the data table. NanoDrop Eight User Guide Thermo Scientific...
Page 87 BCA Setup – Increment the #of standards drop-down and enter the concentration value for the new standard – select Done Edit standard: – from standards measurement screen, seelct BCA Setup Thermo Scientific NanoDrop Eight User Guide...
Page 88 Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 89 (or select Measure if Auto-Measure is off) – lift arm and clean all pedestals with new wipe. 7. When you are finished measuring samples, select End Experiment 8. Lift the arm and clean all pedestals with a new wipe. Thermo Scientific NanoDrop Eight User Guide...
Page 90: Protein Bca Reported Results
• A baseline correction is performed at 750 nm (absorbance value at 750 nm is subtracted from absorbance values at all wavelengths in sample spectrum). • Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 91 Pink dots indicate Orange dots Protein concentration Absorbance standard data points indicate sample at 562 nm data points Standard curve view Thermo Scientific NanoDrop Eight User Guide...
Page 92: Settings For Protein Bca Measurements
You can edit the concentration value for a standard from the application setup screen. After the first sample measurement, these settings cannot be changed. NanoDrop Eight User Guide Thermo Scientific...
Page 93 Note: Replicates setting cannot be changed after the first standard has been measured. Standards Enter actual concentration value of each standard. Note: Concentration values can be entered in any order but the standards must be measured in the order they were entered. Thermo Scientific NanoDrop Eight User Guide...
Page 94 Protein Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 95: Measure Protein Bradford
• Work quickly and do not allow prepared standards or samples to sit longer than necessary. Coomassie dye-dye and Coomassie dye-protein aggregates can form particulates with increasing development time, resulting in significant fluctuations in absorbance readings. Thermo Scientific NanoDrop Eight User Guide...
Page 96 Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 97 7. When you are finished measuring samples, select End Experiment 8. Lift the arm and clean all pedestals with a new wipe. Related Topics • Working with standard curves • Best practices for protein measurements Thermo Scientific NanoDrop Eight User Guide...
Page 98: Protein Bradford Reported Results
• A baseline correction is performed at 750 nm (absorbance value at 750 nm is subtracted from absorbance values at all wavelengths in sample spectrum). • Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 99 Pink dots indicate Orange dots Protein Absorbance standard data points indicate sample concentration at 595 nm data points Standard curve view Thermo Scientific NanoDrop Eight User Guide...
Page 100: Settings For Protein Bradford Measurements
You can edit the concentration value for a standard from the application setup screen. After the first sample measurement, these settings cannot be changed. NanoDrop Eight User Guide Thermo Scientific...
Page 101 Note: Replicates setting cannot be changed after the first standard has been measured. Standards Enter actual concentration value of each standard. Note: Concentration values can be entered in any order but the standards must be measured in the order they were entered. Thermo Scientific NanoDrop Eight User Guide...
Page 102 Protein Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 103: Measure Protein Lowry
Protein assay kits and protocols Please refer to the NanoDrop website for up-to-date kits and protocols for the NanoDrop Eight instrument. Follow the assay kit manufacturer’s recommendations for all standards and samples (unknowns). Ensure each is subjected to the same timing and temperature throughout the assay.
Page 104: To Measure Protein Lowry Standards And Samples
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 105 8. Lift the arm and clean all pedestals with a new wipe. Related Topics • Working with standard curves • Best practices for protein measurements • Measure a Micro-Volume Sample • Prepare Samples and Blanks Thermo Scientific NanoDrop Eight User Guide...
Page 106: Protein Lowry Reported Results
• A baseline correction is performed at 405 nm (absorbance value at 405 nm is subtracted from absorbance values at all wavelengths in sample spectrum). • Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 107 Orange dots indicate Pink dots indicate Protein Absorbance sample data points standard data points concentration at 650 nm Standard curve view Thermo Scientific NanoDrop Eight User Guide...
Page 108: Settings For Protein Lowry Measurements
You can edit the concentration value for a standard from the application setup screen. After the first sample measurement, these settings cannot be changed. NanoDrop Eight User Guide Thermo Scientific...
Page 109 Standards Enter actual concentration value of each standard. Note: Concentration values can be entered in any order but the standards must be measured in the order they were entered. Related Topics • Instrument Settings Thermo Scientific NanoDrop Eight User Guide...
Page 110 Protein Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 111: Measure Protein Pierce 660
The IDCR dissolves completely by thorough mixing and has no effect on the assay. Pre-formulated kits of the protein binding material are available from us or a local distributor. For information about IDCR, refer to the kit manufacturer. Thermo Scientific NanoDrop Eight User Guide...
Page 112: To Measure Protein Pierce 660 Standards And Samples
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 113 7. Lift the arm and clean all pedestals with a new wipe. Related Topics • Working with standard curves • Best practices for protein measurements • Measure a Micro-Volume Sample • Prepare Samples and Blanks • Basic Instrument Operations Thermo Scientific NanoDrop Eight User Guide...
Page 114: Protein Pierce 660 Reported Results
• A baseline correction is performed at 750 nm (absorbance value at 750 nm is subtracted from absorbance values at all wavelengths in sample spectrum). • Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 115 Orange dots indicate Pink dots indicate Protein Absorbance sample data points standard data points concentration at 660 nm Standard curve view Thermo Scientific NanoDrop Eight User Guide...
Page 116: Settings For Protein Pierce 660 Measurements
You can edit the concentration value for a standard from the application setup screen. After the first sample measurement, these settings cannot be changed. NanoDrop Eight User Guide Thermo Scientific...
Page 117 Enter actual concentration value of each standard. Note: Concentration values can be entered in any order but the standards must be measured in the order in which they were entered. Related Topics • Instrument Settings Thermo Scientific NanoDrop Eight User Guide...
Page 118 Protein Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 119: Chapter 6 Measure Od600
The OD600 application measures light transmission and uses that value to calculate absorbance. In spectroscopy, transmitted light is defined as any light that is not absorbed by, reflected from and scattered off a sample. Thermo Scientific NanoDrop Eight User Guide...
Page 120 – Graph the OD600 measurements against the dilution factor The upper detection limit is the measured OD600 value at which there ceases to be a linear correlation between dilution factors and OD600 readings. NanoDrop Eight User Guide Thermo Scientific...
Page 121: To Measure Od600 Samples
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 122 8. When you are finished measuring samples, select End Experiment. 9. Lift the arm and clean all pedestals with a new wipe. Related Topics • Measure a Micro-Volume Sample • Prepare Samples and Blanks • Basic Instrument Operations NanoDrop Eight User Guide Thermo Scientific...
Page 123: Od600 Reported Results
Reported values are shown in the Data table. Select which of the reported results is shown in the data table by selecting from the data table options menu. Here are the available reported values: Thermo Scientific NanoDrop Eight User Guide...
Page 124 Measure OD600 Date/time measured Corrected abs. at 600 nm Absorbance correction Additional wavelength Corrected absorbance at additional wavelength Factor Cell culture concentration (A600 * Factor) Related Topics • Basic Instrument Operations • OD600 Calculations NanoDrop Eight User Guide Thermo Scientific...
Page 125: Settings For Od600 Measurements
Absorbance correction value is subtracted from absorbance values at all wavelengths in sample spectrum. (All displayed absorbance values are corrected values.) Thermo Scientific NanoDrop Eight User Guide...
Page 126 ) * b) in mL/cell-cm where:   ) = molar absorption coefficient (or extinction coefficient) at specified wavelength b = pathlength in cm (1.0 cm for the NanoDrop Eight instruments) Cell number Any number User-defined factor. Generally accepted factor for conversion factor...
Page 127: Calculations For Od600 Measurements
• Displayed spectra and absorbance values are normalized to a 10 mm pathlength equivalent. Reported Values Cell concentration. Reported in cells/mL. Calculations are based on Beer-Lambert equation using corrected A600 absorbance value. Thermo Scientific NanoDrop Eight User Guide...
Page 128 Measure OD600 This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 129: Chapter 7 Custom Applications
Custom Applications Use the NanoDrop Eight to perform UV-Vis measurements. The UV-Vis application allows the instrument to function as a conventional spectrophotometer. Up to 40 wavelengths from 190 nm to 850 nm can be monitored and reported. • Measure UV-Vis ..page 130 •...
Page 130: Measure Uv-Vis
Before you begin... Before taking pedestal measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 131: Best Practices For Uv-Vis Measurements
Ensure samples are homogeneous before taking a measurement. Avoid introducing bubbles when mixing and pipetting. – Follow best practices for micro-volume measurements. – Use a 1-2 µL sample volume. See Recommended Sample Volumes for more information. Thermo Scientific NanoDrop Eight User Guide...
Page 132: Uv-Vis Reported Results
Click sample row to select sample and update spectrum Shift-click multiple sample rows to overlay spectra Click a sample and hover locations on spectra to view measurement values Note Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. NanoDrop Eight User Guide Thermo Scientific...
Page 133 Tips: Click sample row to select sample and update spectrum Shift-click multiple sample rows to overlay spectra Click a sample and hover locations on spectra to view measurement values Thermo Scientific NanoDrop Eight User Guide...
Page 134: Settings For Uv-Vis Measurements
(750 nm) values at all wavelengths in sample spectrum. As a result, absorbance of sample spectrum is zero at specified baseline correction wavelength. NanoDrop Eight User Guide Thermo Scientific...
Page 135: Measure Custom
Before you begin... Before taking measurements with the NanoDrop Eight instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the Pedestals.
Page 136: Delete Custom Method
3. Select 4. Follow the on-screen instructions to measure a sample. Delete Custom Method – From Home screen, from the Custom tab, select Custom Methods. – In Select Method box, select a method to delete NanoDrop Eight User Guide Thermo Scientific...
Page 137: Custom Method Reported Results
Well plate Date/time Click row to select sample options measured and update spectrum. Custom method reported values • Result name • Measurement Range • Analysis wavelength correction Thermo Scientific NanoDrop Eight User Guide...
Page 138: Manage Custom Methods
Baseline correction Manage Custom Methods The NanoDrop Eight software is your tool for creating and managing custom methods, which contain user-defined settings that can be used to acquire data with the instrument. Custom methods can be made with or without standards.
Page 139 – Choose Save Note Any errors in the method will be listed in red text at the bottom of the method editor screen. Errors must be addressed before the method can be saved. Thermo Scientific NanoDrop Eight User Guide...
Page 140 (formula or standards) and Description – From the Custom Method Management screen, select the method you would like to edit from the list of loaded methods. – From the drop-down menu select Edit NanoDrop Eight User Guide Thermo Scientific...
Page 141 • Sloping baseline. Enter two wavelengths that define sloping baseline for analysis correction. (Absorbance value of sloping baseline at analysis wavelength is subtracted from absorbance value at analysis wavelength. Corrected value is used to calculate sample concentration.) Thermo Scientific NanoDrop Eight User Guide...
Page 142 • If specified unit for factor or extinction coefficient is based on mass (such as mg/mL) and specified unit for calculated result is based on molarity (such as pmol/µL) or vice versa, enter molecular weight and use adjacent drop down list to select appropriate unit. NanoDrop Eight User Guide Thermo Scientific...
Page 143 (requires reference measurement and at least standards) – order polynomial: Draws the 3 order least squares polynomial using all measured standards (requires reference measurement and at least three standards) Thermo Scientific NanoDrop Eight User Guide...
Page 144 • When Automated Pathlength is deselected, the software uses a 1 mm pathlength regardless of the sample absorbance. This can cause detector saturation (resulting in jagged peaks) for highly absorbing samples (e.g., ~15 A at 10 mm pathlength equivalent). NanoDrop Eight User Guide Thermo Scientific...
Page 145 • Use period “.” decimal separators for floating point and double-floating point numbers. • Use comma “,” list separators (for example, “POW(2,8)”). • Do not use comma “,” group separators for large numbers (for example, enter 1000 rather than 1,000). Thermo Scientific NanoDrop Eight User Guide...
Page 146 Follow the on-screen instructions to measure a sample. Export Custom Method Export a custom method in order to run it and store the measurement results on another PC for use with another NanoDrop Eight instrument. – From the Custom Methods screen, select a custom method –...
Page 147 Choose Save Delete custom method – From Custom Methods screen, select a custom method from the list of available methods – From the drop-down menu , choose Delete – After the confirmation message, choose Yes Thermo Scientific NanoDrop Eight User Guide...
Page 148 Custom Applications This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 149: Chapter 8 Learning Center
• Measure a Micro-Volume Sample 154 • Sample Modes 158 • Prepare Samples and Blanks 158 • Basic Instrument Operations 164 • Acclaro Sample Intelligence 189 • Instrument Settings 195 • Measurement Screen Display Options 198 Thermo Scientific NanoDrop Eight User Guide...
Page 150: Micro-Volume Sampling-How It Works
Sample Absorbance Sample Concentration Baseline Correction Surface Tension The NanoDrop Eight spectrophotometer uses surface tension to hold a small volume of sample between two pedestals (upper and lower). The patented sample retention system enables the measurement of highly concentrated samples without the need for dilutions.
Page 151 = wavelength-dependent molar absorptivity measurement. This auto-ranging pathlength coefficient (or extinction coefficient) in liter/mol-cm technique produces accurate concentration results over a wide dynamic range. = pathlength in cm = analyte concentration in moles/liter or molarity (M) Thermo Scientific NanoDrop Eight User Guide...
Page 152: Set Up The Instrument
Connect the provided power cord to a grounded wall outlet. See “Power Cords” page 222 for more information. Connect to a Computer Connect the USB cable to the NanoDrop Eight and to an available USB port on your PC. NanoDrop Eight User Guide Thermo Scientific...
Page 153: Operating Specifications
Locate the instrument away from air vents and exhaust fans to minimize evaporation. Note If operating the instrument at the low end of the recommended humidity range, use adequate sample volume to avoid evaporation. After the instrument is installed, you can leave it turned on. Thermo Scientific NanoDrop Eight User Guide...
Page 154: Measure A Micro-Volume Sample
Learning Center Measure a Micro-Volume Sample Measure a Micro-Volume Sample The NanoDrop Eight spectrophotometer uses surface tension to hold a small volume of sample between two pedestals. The patented sample retention system enables the measurement of highly concentrated samples without the need for dilutions.
Page 155: Recommended Sample Volumes
• Do not use hydrofluoric acid (HF) on the pedestals. Fluoride ions will permanently damage the quartz fiber optic cables. 1. From the Home screen, select an application from one of the application categories, such as UV-Vis, or Custom Methods. Thermo Scientific NanoDrop Eight User Guide...
Page 156 Start the sample measurement: – Auto-Measure is On, lower arm – if Auto-Measure is off, lower arm and click Measure – When the sample measurement is completed, the spectra and reported values are displayed. NanoDrop Eight User Guide Thermo Scientific...
Page 157 Acquired data are automatically saved in an experiment with the entered name. In the default configuration, experiments are stored in a database according to acquisition date, experiment name, application used any assigned labels (see Manage identifiers). Thermo Scientific NanoDrop Eight User Guide...
Page 158: Sample Modes
Sample Modes Sample Modes The NanoDrop Eight can be used in either Single sample or an Eight sample mode. Select the desired mode from the drop-down menu on the Home screen. In Single Sample mode, measurements will only be taken using Channel A.
Page 159: Preparing Samples
It is not necessary to blank the instrument before each sample measurement unless the samples are dissolved in different buffer solutions. • It is recommended to measure a new blank every 30 minutes. Thermo Scientific NanoDrop Eight User Guide...
Page 160 “mirror image” spectrum • Sample was inadvertently used to blank instrument. (Resulting sample spectra may exhibit negative absorbance values or, in some cases, resemble a mirror image of a typical pure nucleic acid or protein spectrum.) NanoDrop Eight User Guide Thermo Scientific...
Page 161 The blanking solution should be a similar pH and ionic strength as the analyte solution. For details, see “To measure samples” in the application used. Thermo Scientific NanoDrop Eight User Guide...
Page 162: Run A Blanking Cycle
• Do not use a squirt or spray bottle on or near the instrument as liquids will flow into the instrument and may cause permanent damage. • Do not use hydrofluoric acid (HF) on the pedestals. Fluoride ions will permanently damage the quartz fiber optic cables. NanoDrop Eight User Guide Thermo Scientific...
Page 163 Protein A280 protein quantification specifications, see Solutions for Blanking Problems. 5. When you are finished with the blanking cycle, select End Experiment. 6. Lift the arm and clean all pedestals with a new wipe. Thermo Scientific NanoDrop Eight User Guide...
Page 164: Basic Instrument Operations
NanoDrop Eight Home Screen • NanoDrop Eight Measurement Screens • View History • NanoDrop Eight General Operations NanoDrop Eight Home Screen These operations are available from the NanoDrop Eight Home screen. Applications System Status Application categories Control options SciVault History Instrument Diagnostics...
Page 165 Learning Center Basic Instrument Operations Applications The NanoDrop Eight software offers several configurable applications, which gives users full control of the measurement. See“Custom Applications” page 129 detailed information about each available application. System Status Select the icon on the Home screen to open the system status box.
Page 166 SciVault Software The Thermo Scientific™ SciVault™ software is available as an optional add-on. This companion software allows users to operate their NanoDrop Eight instrument in a manner that complies with US FDA 21 CFR Part 11. When purchased, the SciVault software is shipped to you on a USB stick and integrates directly into the NanoDrop Eight software user interface.
Page 167: Nanodrop Eight Measurement Screens
Learning Center Basic Instrument Operations NanoDrop Eight Measurement Screens These operations are available from any measurement screen within an Application. Application Import View measurement Measure blank End experiment and type Sample ID history solution export data Auto- Measure UV absorbance...
Page 168: Measurement Screen Display Options
Found peaks for the defined range are listed in the table below the spectrum. Wavelength start Wavelength end Absorbance minimum UV spectrum Peak 1 Table of calculated peaks for the specified range Maximum number of peaks NanoDrop Eight User Guide Thermo Scientific...
Page 169: Sample Name
The types of results that appear in the measurement screens depend on the selected application. For details, see the reported results section of that application in this guide: Applications > [application group] > Measure [application name] > Reported Results Thermo Scientific NanoDrop Eight User Guide...
Page 170 Micro-volume absorbance measurements are normalized to a 10.0 mm pathlength equivalent. Measurement Alerts Acclaro Sample Intelligence technology built into the NanoDrop Eight instrument provides important features to help you assess sample integrity. click a Sample Intelligence icon in the software to view its associated information. contaminant analysis...
Page 171: Measure Button
Auto-Measure and Auto-Blank Options Speed up sample analysis with the NanoDrop Eight Auto-Measure and Auto-Blank features, which cause the instrument to start the measurement immediately after you lower the instrument arm. These options eliminate the need for repetitive Measure or Blank operations for large batches of samples.
Page 172 Tags Enter a descriptive label to help you find this experiment later or to associate it with another experiment (see Manage identifiers on the instrument for details). NanoDrop Eight User Guide Thermo Scientific...
Page 173 Available export file formats: • comma-separated values spreadsheet (.csv) file • tab-separated values spreadsheet (.tsv) file • NanoDrop Eight software (.n8db) file The filename is the entered experiment name (see above). The file is stored in a folder named “NanodropEight”...
Page 174: Data Table
• 1.5 mL tubes: allows users to keep track of samples measurements for samples stored in the 1.5 mL-sized spaces in the NanoDrop Eight tube rack accessory • 0.5 mL tubes: allows users to keep track of samples measurements for samples stored in the 0.5 mL-sized spaces in the NanoDrop Eight tube rack accessory...
Page 175 Sample channels errors Currently active channel with sample IDs populated Dark green indicates Dark orange indicates Measurement inactive well with completed with sample ID populated Well plate map shown in the measurement screen no errors Thermo Scientific NanoDrop Eight User Guide...
Page 176: View History
Whether you collect one sample or many in a row, after you choose End Experiment, the acquired data are automatically saved in an experiment with an experiment name. In the default configuration, experiments are stored in the NanoDrop Eight database according to acquisition date, experiment name,...
Page 177 Learning Center Basic Instrument Operations Open instrument database of measurement results – to open NanoDrop Eight database, from the Home screen, select History. History Menu Available options: Home Return to NanoDrop Eight Home screen Import Import data from a USB flash drive or folder on your...
Page 178 Use Select in History to select experiments to be exported. Export selected experiments – Open History. You can filter or use the Search feature to find experiment Search – click the checkbox to select row or rows to be exported – click Export NanoDrop Eight User Guide Thermo Scientific...
Page 179 (click again to deselect an experiment) – Click Delete and OK Note Deleted data cannot be recovered. Open Experiment and View Associated Data Use History to locate and open any experiment to see the measurement data it contains. Thermo Scientific NanoDrop Eight User Guide...
Page 180 Selected experiment Selected application Menu of options; click to open UV spectrum for selected sample(s) Click row to select sample and display spectrum. Select multiple Measurement results; see rows to overlay spectra Applications for details NanoDrop Eight User Guide Thermo Scientific...
Page 181: Nanodrop Eight General Operations
Select the menu in the upper right corner from any Spectral Data or Data Table screen to see the available menu options. Home Return to NanoDrop Eight Home screen Manage Identifiers Add or delete labels for selected experiment to make it...
Page 182 Edit Experiment Name You can edit the experiment name when you save the experiment or afterwards from the History. Edit experiment name at end of experiment – when finished measuring samples, select End Experiment NanoDrop Eight User Guide Thermo Scientific...
Page 183 • as tab-separated values (.tsv) files containing: – whole spectrum data in columns – report data in columns – both report and spectrum data combined in columns Thermo Scientific NanoDrop Eight User Guide...
Page 184 – whole spectrum data in single column for TQ Analyst • as NanoDrop Eight software (.n8db) files containing spectra and measurement results for each exported experiment Use any spreadsheet or word processing application to open a CSV or TSV file. Here...
Page 185 Click the checkbox for the experiment(s) you want to export. You can use the Search feature to find experiment – Click Export – Select one or more formats to export to (see above for details) – Set File Path: to an available export path and click Export Thermo Scientific NanoDrop Eight User Guide...
Page 186 – select row in History. You can filter experiments by date or type, or use Search feature to find desired experiment – click to select one or more experiments to export – click Delete NanoDrop Eight User Guide Thermo Scientific...
Page 187 History or use Search feature to find desired experiment – click the experiment name to open the experiment – click the menu in the upper right corner of the screen and choose Print Thermo Scientific NanoDrop Eight User Guide...
Page 188 Note The software saves the print settings each time you print. – choose Print The selected measurement screen is printed for each selected measurement. NanoDrop Eight User Guide Thermo Scientific...
Page 189: Acclaro Sample Intelligence
Acclaro Sample Intelligence Acclaro Sample Intelligence The Thermo Scientific™ Acclaro™ Sample Intelligence technology built into the NanoDrop Eight instrument provides these exclusive features to help you assess sample integrity: contaminant analysis to help qualify a sample before use in downstream...
Page 190 The icons appear in the Sample Plate Map, the data table, and in History (see below). The icons are active in all three places; the information remains with the data indefinitely, even after it has been exported. NanoDrop Eight User Guide Thermo Scientific...
Page 191: Contaminant Analysis
Learning Center Acclaro Sample Intelligence Contaminant Analysis For the dsDNA, RNA and Protein A280 applications, the NanoDrop Eight software automatically initiates a spectral analysis for several known contaminants during the measurement. Examples of known contaminants include: • for dsDNA and RNA measurements: –...
Page 192 • original nucleic acid concentration (462.6 ng/µL), which is based on the total baseline-corrected absorbance (sample plus contaminant) at the analysis wavelength • corrected nucleic acid concentration (286.4 ng/µL), which is based on the corrected absorbance (sample minus contaminant) at the analysis wavelength NanoDrop Eight User Guide Thermo Scientific...
Page 193 Note Achieving consistent, high quality contaminant analysis results is dependent on the quality of the measured sample spectra, which is dependent on the maintenance status of the instrument. For more information, see Maintenance Schedule. Thermo Scientific NanoDrop Eight User Guide...
Page 194: On-Demand Technical Support
Learning Center Acclaro Sample Intelligence On-Demand Technical Support For the dsDNA and Protein A280 applications, the NanoDrop Eight software monitors all sample measurements for the presence of contaminants or other anomalies that may affect the measurement. Examples of monitored characteristics include: •...
Page 195: Instrument Settings
Dye Editor, Protein Editor, and Preferences. System Settings These options are available: Database The NanoDrop Eight uses a built-in database Security Used when the optional Thermo Scientific™ SciVault™ software is installed. The server location is automatically populated for single computer installations, but must be Copy and Pasted for different computer installations.
Page 196: Database Backup And Restore
You can backup and restore the measurement database to a specified location of your choosing. Configure database backup From the Settings screen, in the Database Backup & Restore region, select Configure. The current backup location is displayed. Click Browse to assign the backup location. NanoDrop Eight User Guide Thermo Scientific...
Page 197 Restore database from backup To restore data from a previous backup event, from Database Maintenance, select Restore and browse for the database backup you wish to use. Once you have selected your backup, click the Restore button. Thermo Scientific NanoDrop Eight User Guide...
Page 198: Preferences
Hover spectrum to see plot data Display graph legend Calculate peaks for specified range Scale axes to fit spectra measurement Select to manually enter x-axis range Select to manually enter y-axis range Display options- Right click graph to view NanoDrop Eight User Guide Thermo Scientific...
Page 199 Found peaks for the defined range are listed in the table below the spectrum. Wavelength start Wavelength end Absorbance minimum UV spectrum Peak 1 Table of calculated peaks for the specified range Maximum number of peaks Thermo Scientific NanoDrop Eight User Guide...
Page 200 Learning Center This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 201: Chapter 9 Maintenance
Maintenance • Maintenance Schedule 202 • Maintaining the Pedestals 203 • Decontaminating the Instrument 207 • Instrument Diagnostics 209 Thermo Scientific NanoDrop Eight User Guide...
Page 202: Maintenance Schedule
If the issue persists, contact us. If you are outside the U.S.A. and Canada, please contact your local distributor. If your instrument requires maintenance or repair, contact us or your local distributor. NanoDrop Eight User Guide Thermo Scientific...
Page 203: Maintaining The Pedestals
If the diaphragm becomes loose, contact Note Solutions containing detergent or isopropyl alcohol may uncondition the pedestals. If these are required for sample analyses, follow immediately with 3– 5 µL DI H Thermo Scientific NanoDrop Eight User Guide...
Page 204 PR-1 compound. If you do not have PR-1, you can also substitute 0.5M HCl for the DI H O in the procedure above and follow with 3 uL DI H NanoDrop Eight User Guide Thermo Scientific...
Page 205: Reconditioning The Pedestals
Properly conditioned pedestal (droplet flattens out) (droplet beads up) Supplies needed • lint-free laboratory wipes • PR-1 pedestal reconditioning kit (available from us or a local distributor) • calibrated precision pipettor (0-2 µL) • canned air Thermo Scientific NanoDrop Eight User Guide...
Page 206 6. Pipette 1 µL DI H O onto the lower pedestals. The DI H O should “bead up” or form a rounded droplet. Droplet “beads up” on properly conditioned pedestal NanoDrop Eight User Guide Thermo Scientific...
Page 207: Decontaminating The Instrument
• Do not allow HCl, alcohol, bleach, acetone or any other solvent to remain on the diaphragm for more than one minute or it may loosen the seals. If the diaphragm becomes loose, contact • Thermo Scientific NanoDrop Eight User Guide...
Page 208: Supplies Needed
(see Supplies needed) and use it to gently wipe the outside surfaces of the instrument. 2. Use a clean cloth or wipe dampened with DI H O to remove the bleach solution. NanoDrop Eight User Guide Thermo Scientific...
Page 209: Instrument Diagnostics
Maintenance Instrument Diagnostics Instrument Diagnostics Every 6 months, run the following performance and quality checks to verify instrument operation. Intensity Check 210 Performance Verification 212 Thermo Scientific NanoDrop Eight User Guide...
Page 210: Intensity Check
Maintenance Instrument Diagnostics Diagnostics can be performed using the NanoDrop Eight software. Intensity Check and Performance Verification, are all accessible from the software Home screen: Figure 1. Control options History: View data stored locally. Filter by date or application. Performance:...
Page 211 Intensity Check. If a yellow triangle appears next to the Bias indicator, make sure the room is within the temperature specifications for the instrument. If the Intensity Check fails again, contact Thermo Scientific NanoDrop Eight User Guide...
Page 212: Performance Verification
The droplets should “bead up” as shown below. If it does not, recondition the pedestals. Remove the water sample from the upper and lower pedestal surfaces with a dry laboratory wipe. Droplets “bead up” on properly conditioned pedestals NanoDrop Eight User Guide Thermo Scientific...
Page 213 Instrument Diagnostics Sample Loading Hints • Ensure the NanoDrop Eight instrument is not situated near an air vent or an exhaust fan from a nearby instrument. • Use a small-volume (0.5 - 10 µL) 8-channel pipettor to load the diH 0 and the PV-1 aliquots.
Page 214 If results fail to meet specifications using 2 µL aliquots, contact support or local distributor for assistance. 2. Click End Experiment when done. a. Results can be exported and printed at this time or later from the History. NanoDrop Eight User Guide Thermo Scientific...
Page 215 3. Click End Experiment when done. 4. To review results from a previous Performance Verification check, select History from the Home screen and locate the Performance Verification check results from the list of experiments. Thermo Scientific NanoDrop Eight User Guide...
Page 216 Maintenance This page is intentionally blank. NanoDrop Eight User Guide Thermo Scientific...
Page 217: Chapter 10 Safety And Operating Precautions
Safety and Operating Precautions Contents • Operating Precautions 218 • Safety Information 219 Note Be sure that all persons operating this system read the safety manual first. Thermo Scientific NanoDrop Eight User Guide...
Page 218: Operating Precautions
The instrument warranty is void if the cover has been removed. NanoDrop Eight spectrophotometers are designed to operate indoors in an environment that meets our specifications. For details, see the site preparation guide for your instrument.
Page 219: Safety Information
Safety and Operating Precautions Safety Information Safety Information Before operating a NanoDrop Eight instrument, please read the safety information and follow its recommendations for the system. Safety and Special Notices In many cases, safety information is displayed on the instrument itself. The symbol indicates that there is additional safety information in the documentation and failure to heed the safety precautions could result in injury.
Page 220 Use approved containers and proper procedures to dispose of waste. Symbol Description Alternating current Earth terminal or ground Direct current Protective conductor terminal Frame or chassis terminal Fuse Power on Power off NanoDrop Eight User Guide Thermo Scientific...
Page 221: When The System Arrives
Utility installations must comply with all local building and safety codes. Lifting or Moving the Instrument To avoid risk of injury, use proper lifting techniques when lifting or moving the instrument or other system components. Thermo Scientific NanoDrop Eight User Guide...
Page 222: Electrical Requirements And Safety
Be sure to use an appropriate grounded power cord for your electrical service. If the power cord received is not appropriate for the electrical system in your location, or if the power cord becomes damaged, contact us. Power Line Conditioning Accessories NanoDrop Eight User Guide Thermo Scientific...
Page 223: Fire Safety And Burn Hazards
• Use caution when testing flammable or explosive samples (see the “Hazardous Materials” section) • Never block any of the vents on the instrument or its power supply • Only use exact replacement power supplies from us Thermo Scientific NanoDrop Eight User Guide...
Page 224: Optical Safety
• carbon tetrachloride • DMSO • DMF • acetonitrile • THF • toluene • hexane • benzene • sodium hydroxide • sodium hypochlorite (bleach) • dilute HCl • dilute HNO • dilute acetic acid NanoDrop Eight User Guide Thermo Scientific...
Page 225 O sample to ensure that solvents are not inadvertently left on the pedestal. The diaphragm around the pedestal of the NanoDrop Eight is permanently affixed to the instrument. Do not attempt to remove the diaphragm or break the seal. Avoid prolonged exposure of the diaphragm to HCl, alcohol, bleach, acetone or other solvents as the adhesive securing the seal may be affected.
Page 226 Contact us if you have questions about decontamination requirements. NanoDrop Eight User Guide Thermo Scientific...

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