Voyager DP-263-S User's Guide

User’s GuideVersion 5 Series SoftwarePerSeptive Biosystems, Inc.500 Old Connecticut PathFramingham, MA 01701 USAA subsidiary of PE CorporationPart Nu

Table of Contentsx PerSeptive BiosystemsChapter 7 PSD Analysis7.1 Overview of PSD Analysis...

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-22 PerSeptive Biosystems2Video monitorsFigure 2-12 and Figure 2-13 show the re

Connecting the Voyager-DE STR WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 2-232NOTE: In the US only, you can plug the video monitor

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-24 PerSeptive Biosystems22.5 Installing SoftwareAll necessary software is ins

Installing SoftwareVoyager™ Biospectrometry™ Workstation User’s Guide 2-2522.5.1 Installing the Voyager SoftwareInstallingTo install the Voyager soft

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-26 PerSeptive Biosystems2• User Guides—Includes PDF (portable document format)

Installing SoftwareVoyager™ Biospectrometry™ Workstation User’s Guide 2-2722.5.2 Starting the SoftwareStartingInstrumentControl PanelTo start the Voy

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-28 PerSeptive Biosystems2StartingSequence ControlPanelTo start the Sequence Co

Installing SoftwareVoyager™ Biospectrometry™ Workstation User’s Guide 2-2922.5.3 Exiting the SoftwareCAUTIONIf you are using the Voyager Workstation

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-30 PerSeptive Biosystems22.6 Hardware ConfigurationCAUTIONDo not alter the Ha

Hardware ConfigurationVoyager™ Biospectrometry™ Workstation User’s Guide 2-312.Figure 2-16 Vacuum Configuration3. Check the following values as neede

Table of ContentsVoyager Biospectrometry Workstation User’s Guide xiAppendix A Specifications...

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-32 PerSeptive Biosystems2• Source Chamber (BA1) Wait Time—Time (seconds) that

Hardware ConfigurationVoyager™ Biospectrometry™ Workstation User’s Guide 2-332High voltageconfigurationTo check high voltage configuration:1. In the I

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-34 PerSeptive Biosystems2• Idle Power Off/Idle Time—When enabled, the number o

Hardware ConfigurationVoyager™ Biospectrometry™ Workstation User’s Guide 2-3523. Check the following values as needed:• Flight Length to Deflector (Re

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-36 PerSeptive Biosystems23. Check the following fields as needed:• Instrument

Hardware ConfigurationVoyager™ Biospectrometry™ Workstation User’s Guide 2-372Figure 2-20 Laser Configuration3. Check the following fields as needed:

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-38 PerSeptive Biosystems2DigitizerconfigurationTo check the configuration of t

Aligning the Sample PlateVoyager™ Biospectrometry™ Workstation User’s Guide 2-3922.7 Aligning the Sample PlateIn this sectionThis section describes:•

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-40 PerSeptive Biosystems2.PLT files andmultiplealignmentsA .PLT file defines t

Aligning the Sample PlateVoyager™ Biospectrometry™ Workstation User’s Guide 2-412Overview of videomonitor displayThe following examples show how the s

Table of Contentsxii PerSeptive Biosystems

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-42 PerSeptive Biosystems2What you needTo align the sample plate you need the f

Aligning the Sample PlateVoyager™ Biospectrometry™ Workstation User’s Guide 2-432Using the controlstickTo align a sample plate, you must use the contr

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-44 PerSeptive Biosystems2Figure 2-26 Sample Plate Alignment Wizard3. Click Ne

Aligning the Sample PlateVoyager™ Biospectrometry™ Workstation User’s Guide 2-452The software calculates the alignment and uses the settings to ensure

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-46 PerSeptive Biosystems22.8 Startup and ShutdownIn this sectionThis section

Startup and ShutdownVoyager™ Biospectrometry™ Workstation User’s Guide 2-472If your system includes a LeCroy digitizer, wait approximately one minute

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-48 PerSeptive Biosystems2InitializingThe hardware is automatically initialized

Startup and ShutdownVoyager™ Biospectrometry™ Workstation User’s Guide 2-492Powering downthe massspectrometerIf you need to perform maintenance on int

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-50 PerSeptive Biosystems22.9 Checking System StatusDisplay the System Status

Checking System StatusVoyager™ Biospectrometry™ Workstation User’s Guide 2-512Table 2-2 System Status ParametersParameter DescriptionSystem StatusIn

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xiii1Safety and Compliance InformationIn this sectionThis section

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-52 PerSeptive Biosystems2

3ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 3-13 Preparing SamplesThis chapter contains the following sections:3.1 Preparing Samples

Chapter 3 Preparing Samples3-2 PerSeptive Biosystems33.1 Preparing Samples NOTE: Sample preparation is critical to obtain good results in MALDI-T

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-333.1.1 Selecting a MatrixPurpose of matrixIn MALDI-TOF, the matrix plays a key

Chapter 3 Preparing Samples3-4 PerSeptive Biosystems3MixturesIf you are examining a sample mixture, it may be necessary to prepare the mixture wit

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-53NOTE: HPLC-grade water may vary in salt concentration and may produce adduct i

Chapter 3 Preparing Samples3-6 PerSeptive Biosystems35. Cap the tube and vortex thoroughly for approximately 1 minute or until dissolved. You can

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-73Sinapinic acidUse sinapinic acid for peptides and proteins >10,000 Da.Matri

Chapter 3 Preparing Samples3-8 PerSeptive Biosystems3CHCAUseα-cyano-4-hydroxycinnamic acid (CHCA) for:• Dried drop application—Peptides/proteins &

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-93CHCA for thin layerapplicationUse for peptides <3,000 Da.Matrix concentrati

Safety and Compliance Informationxiv PerSeptive Biosystems1A Caution provides information to avoid damage to the system or loss of data and appears as

Chapter 3 Preparing Samples3-10 PerSeptive Biosystems3THAPUse THAP for small oligonucleotides <3,500 Da, acidic carbohydrates, acidic glycopept

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-1133-HPAUse 3-HPA for large oligonucleotides >3,500 Da.Matrix concentration 5

Chapter 3 Preparing Samples3-12 PerSeptive Biosystems3DHBUse DHB for:• Neutral carbohydrates• Small moleculesDHB for neutralcarbohydratesMatrix co

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-133DHB for smallmoleculesMatrix concentration 10 mg/mlFinal sample concentration

Chapter 3 Preparing Samples3-14 PerSeptive Biosystems3DHBsUse DHBs for peptides and proteins >10,000 Da, and glycosylated proteins.Matrix conce

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-153Synthetic polymermatricesChoice of matrix depends on the sample you are analy

Chapter 3 Preparing Samples3-16 PerSeptive Biosystems3You can load polymer samples on sample plates in two ways:• Thin layer polymer method (yield

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-1733.1.4 Preparing SampleIn this sectionThis section includes:• Sample concentr

Chapter 3 Preparing Samples3-18 PerSeptive Biosystems3Note the following:• When diluting sample, keep in mind that you will be further diluting wh

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-1933.1.5 Sample CleanupCleaningtechniquesUse the following techniques to clean

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xv1Safety symbolsThe following symbols may be displayed on the sys

Chapter 3 Preparing Samples3-20 PerSeptive Biosystems33.1.5.1 WashingWhen to useUse this technique when you know the solubility of the contaminan

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-2133.1.5.2 Drop Dialysis (Floating Membrane)When to useUse this technique on po

Chapter 3 Preparing Samples3-22 PerSeptive Biosystems3NOTE: Sample also passes through the membrane during dialysis, particularly low mass samples

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-2333.1.5.3 Cation ExchangeWhen to useUse this technique for non-polar proteins

Chapter 3 Preparing Samples3-24 PerSeptive Biosystems33.1.5.4 ZipTips® When to useUse this technique for peptides, proteins, and oligonucleotides

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-253ProcedureTo clean samples with ZipTips:1. Wash a C18 ZipTip in the following

Chapter 3 Preparing Samples3-26 PerSeptive Biosystems33.1.6 Mixing Sample and Matrix (Dried Droplet Application)When to useUse dried droplet appl

Preparing SamplesVoyager™ Biospectrometry™ Workstation User’s Guide 3-273Mixing sampleand matrix on thesample plateMix sample and matrix directly on t

Chapter 3 Preparing Samples3-28 PerSeptive Biosystems33.2 Loading Samples on Sample PlatesIn this sectionThis section describes:•Overview• Loadin

Loading Samples on Sample PlatesVoyager™ Biospectrometry™ Workstation User’s Guide 3-293Types of sampleplatesThree types of 100-position reusable samp

Safety and Compliance Informationxvi PerSeptive Biosystems1Non-electricalSymbolsThe following is an illustrated glossary of non-electrical safety aler

Chapter 3 Preparing Samples3-30 PerSeptive Biosystems3Handling sampleplatesTo prevent contamination of your analysis:• Start with a clean sample p

Loading Samples on Sample PlatesVoyager™ Biospectrometry™ Workstation User’s Guide 3-3133.2.2 Loading Samples (Dried Droplet Application)NOTE: If you

Chapter 3 Preparing Samples3-32 PerSeptive Biosystems3Do not touch the tip of the pipette to the sample spot. Make sure the sample is evenly appli

Loading Samples on Sample PlatesVoyager™ Biospectrometry™ Workstation User’s Guide 3-3333.2.3 Loading Samples (Thin Layer Application)When to useUse

Chapter 3 Preparing Samples3-34 PerSeptive Biosystems33.2.4 Examining Crystals on Sample PlatesOverviewIf you are using polished blank or laser e

Loading Samples on Sample PlatesVoyager™ Biospectrometry™ Workstation User’s Guide 3-353You can acquire data from a well that does not have an ideal c

Chapter 3 Preparing Samples3-36 PerSeptive Biosystems33.3 Cleaning Sample PlatesIn this sectionThis section describes procedures for cleaning:•Te

Cleaning Sample PlatesVoyager™ Biospectrometry™ Workstation User’s Guide 3-3736. Examine the plate. If you see any sample or matrix residue, oil, or f

Chapter 3 Preparing Samples3-38 PerSeptive Biosystems3CAUTIONDo not leave the sample plate in detergent for longer than 10 minutes. Longer exposur

Loading Sample Plates in the Mass SpectrometerVoyager™ Biospectrometry™ Workstation User’s Guide 3-3933.4 Loading Sample Plates in the Mass Spectrome

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xvii1Symboles desalertes desécuritéLes symboles suivants peuvent ê

Chapter 3 Preparing Samples3-40 PerSeptive Biosystems3Table 3-1 Sample Plate InformationParameter DescriptionPlate ID Unique identifier (up to 3

Loading Sample Plates in the Mass SpectrometerVoyager™ Biospectrometry™ Workstation User’s Guide 3-4133.4.1 Ejecting the Sample HolderIn the Voyager

Chapter 3 Preparing Samples3-42 PerSeptive Biosystems33.4.2 Loading Sample PlatesThis section describes loading sample plates in:• Voyager-DE and

Loading Sample Plates in the Mass SpectrometerVoyager™ Biospectrometry™ Workstation User’s Guide 3-433Figure 3-5 Loading the Sample Plate in a Voyage

Chapter 3 Preparing Samples3-44 PerSeptive Biosystems35. Select a Plate ID. The .PLT file and alignment information associated with the Plate ID a

Loading Sample Plates in the Mass SpectrometerVoyager™ Biospectrometry™ Workstation User’s Guide 3-453Figure 3-7 Loading the Sample Plate in a Voyage

Chapter 3 Preparing Samples3-46 PerSeptive Biosystems35. Select a Plate ID. The .PLT file and alignment information associated with the Plate ID a

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-4733.5 Sample Plate Types SupportedIn addition to 100-position reusa

Chapter 3 Preparing Samples3-48 PerSeptive Biosystems33.5.1 Sample Plates Types and ApplicationsThe Voyager Instrument Control software supports

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-493NOTE: For additional information on available sample plates and or

Safety and Compliance Informationxviii PerSeptive Biosystems1Symboles nonélectriquesLe tableau suivant donne la signification des symboles d’alertes d

Chapter 3 Preparing Samples3-50 PerSeptive Biosystems33.5.2 Editable-Configuration Plate (.PLT) Types Provided with the SystemSelecting platetype

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-513.PLT filesprovidedThe editable-configuration plate types provided

Chapter 3 Preparing Samples3-52 PerSeptive Biosystems33.5.3 Guidelines forDefining Custom Plate TypesYou can define custom plate types of unlimit

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-533A .PLT file describes each position on the plate as discussed in T

Chapter 3 Preparing Samples3-54 PerSeptive Biosystems3X and Y Coordinates of the position center in reference to the lower left corner of the samp

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-553Width Use if you are customizing a .PLT file. Defines the width of

Chapter 3 Preparing Samples3-56 PerSeptive Biosystems3Figure 3-11 illustrates the coordinates for the four corner positions that define the edges

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-573Guidelines forcreating .PLT filesNote the following:• The diameter

Chapter 3 Preparing Samples3-58 PerSeptive Biosystems3NOTE: You can correct for systematic errors introduced by a sample preparation device by ali

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-593Tolerances andnon-systematicerrorsWhen creating search pattern fil

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xix1Before operatingthis instrumentEnsure that anyone involved wit

Chapter 3 Preparing Samples3-60 PerSeptive Biosystems3Figure 3-12 Area Available for AnalysisHow to create a.PLT fileNOTE: Display the Sample Vie

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-613Figure 3-13 shows the Plate View displaying the logical coordinate

Chapter 3 Preparing Samples3-62 PerSeptive Biosystems38. On the second line, type in absolute coordinates for the first position. Separate absolut

Sample Plate Types SupportedVoyager™ Biospectrometry™ Workstation User’s Guide 3-6333.5.4 Adjusting the Laser Position for a Custom .PLT File After y

Chapter 3 Preparing Samples3-64 PerSeptive Biosystems3

4ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 4-14 Voyager Instrument Control Panel BasicsThis chapter contains the following sections:4

Chapter 4 Voyager Instrument Control Panel Basics4-2 PerSeptive Biosystems44.1 Instrument Control PanelThe Voyager Instrument Control Panel allow

Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 4-34Figure 4-1 Instrument Control PanelToolbarThe toolbar contains buttons

Chapter 4 Voyager Instrument Control Panel Basics4-4 PerSeptive Biosystems4Control pagesThe Instrument Control Panel contains five control pages:•

Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 4-54Spectrum windowThe Spectrum window provides a display of data. The data

NOTICEPerSeptive Biosystems, Inc. supplies or recommends certain configurations of computer hardware, software, and peripherals for use with its instr

Safety and Compliance Informationxx PerSeptive Biosystems1General WarningsWARNINGFIRE HAZARD. Using a fuse of the wrong type or rating can cause a fir

Chapter 4 Voyager Instrument Control Panel Basics4-6 PerSeptive Biosystems4DisplayingThe Output window is automatically displayed when you:• Acqui

Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 4-74Automatic controlmodeTo select Automatic Control mode:1. Open the Instr

Chapter 4 Voyager Instrument Control Panel Basics4-8 PerSeptive Biosystems44.2 Using the Control PagesThe Instrument Control Panel allows you to

Using the Control PagesVoyager™ Biospectrometry™ Workstation User’s Guide 4-94Types of pagecontrolYou can select between two types of page control for

Chapter 4 Voyager Instrument Control Panel Basics4-10 PerSeptive Biosystems44.3 Using the Spectrum WindowThis section includes:• Adjusting the di

Using the Spectrum WindowVoyager™ Biospectrometry™ Workstation User’s Guide 4-1144. Set From and To values for the display range (m/z units) and click

Chapter 4 Voyager Instrument Control Panel Basics4-12 PerSeptive Biosystems47. Set as needed:8. Click OK.Parameter DescriptionScaling ModeDisplay

Using the Spectrum WindowVoyager™ Biospectrometry™ Workstation User’s Guide 4-1344.3.2 Zooming on TracesZooming andunzoomingYou can expand (zoom) an

Chapter 4 Voyager Instrument Control Panel Basics4-14 PerSeptive Biosystems4Types of tracesThe Spectrum window can contain two types of traces (se

Using the Spectrum WindowVoyager™ Biospectrometry™ Workstation User’s Guide 4-154Hint: Resize the window to view all added traces.Figure 4-5 Adding T

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xxi1WARNINGELECTRICAL SHOCK HAZARD. Severe electrical shock can re

Chapter 4 Voyager Instrument Control Panel Basics4-16 PerSeptive Biosystems44.3.4 Annotating TracesThis section describes:• Two ways to annotate•

Using the Spectrum WindowVoyager™ Biospectrometry™ Workstation User’s Guide 4-174Hint: To move the text, left-click and hold on the text, then drag to

Chapter 4 Voyager Instrument Control Panel Basics4-18 PerSeptive Biosystems44.3.5 Previewing and Printing TracesThis section includes:• Previewin

Using the Spectrum WindowVoyager™ Biospectrometry™ Workstation User’s Guide 4-194NOTE: If you set Landscape printing orientation within Instrument Con

Chapter 4 Voyager Instrument Control Panel Basics4-20 PerSeptive Biosystems4Dedicating aprinter tolandscapeorientationTo dedicate the printer to l

Customizing the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 4-2144.4 Customizing the Instrument Control PanelUndocking

Chapter 4 Voyager Instrument Control Panel Basics4-22 PerSeptive Biosystems4Accessinggraphic optionsTo access the graphic options:1. Display the t

Customizing the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 4-234Figure 4-6 Graph and Plot Options Dialog BoxFor addit

Chapter 4 Voyager Instrument Control Panel Basics4-24 PerSeptive Biosystems44.5 Controlling the WorkstationThis section includes:• Using toolbar

Controlling the WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 4-254Turninghigh voltage onand offClick in the toolbar to turn the hig

Safety and Compliance Informationxxii PerSeptive Biosystems1WARNINGPHYSICAL INJURY HAZARD. Use the Voyager Biospectrometry Workstation only as specifi

Chapter 4 Voyager Instrument Control Panel Basics4-26 PerSeptive Biosystems4AccumulatingspectraClick in the toolbar to manually accumulate spect

Controlling the WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 4-2744.5.2 Adjusting Laser Intensity and Selecting Sample PositionThis

Chapter 4 Voyager Instrument Control Panel Basics4-28 PerSeptive Biosystems4The Manual Laser/Sample Position control page allows you to:• Manually

Controlling the WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 4-294Selecting theactive sampleposition in PlateviewThe active sample po

Chapter 4 Voyager Instrument Control Panel Basics4-30 PerSeptive Biosystems4You can use these coordinates when you create a search pattern file. F

Controlling the WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 4-314Hint: If you right-click on a position, you can change between Samp

Chapter 4 Voyager Instrument Control Panel Basics4-32 PerSeptive Biosystems44.6 Sequence Control PanelSequence ControlPanelThe Voyager Sequence C

How the Instrument and Sequence Control Panels InteractVoyager™ Biospectrometry™ Workstation User’s Guide 4-334When you start the Sequence Control Pan

Chapter 4 Voyager Instrument Control Panel Basics4-34 PerSeptive Biosystems4If you start the Instrument Control Panel using the Sequence Control P

How the Instrument and Sequence Control Panels InteractVoyager™ Biospectrometry™ Workstation User’s Guide 4-354Keeping bothcontrol panelsopenYou can k

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xxiii1Safety and EMC (Electromagnetic Compliance) StandardsUS Safe

Chapter 4 Voyager Instrument Control Panel Basics4-36 PerSeptive Biosystems4

5ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 5-1]75 OptimizingInstrument SettingsThis chapter contains the following sections:5.1 Load

Chapter 5 Optimizing Instrument Settings5-2 PerSeptive Biosystems55.1 Loading, Modifying, and Saving Instrument SettingsThis section includes:• U

Loading, Modifying, and Saving Instrument SettingsVoyager™ Biospectrometry™ Workstation User’s Guide 5-35NOTE: Data storage parameters are not stored

Chapter 5 Optimizing Instrument Settings5-4 PerSeptive Biosystems5List of .BIC filesTable 5-1 through Table 5-3 list the standard .BIC files provi

Loading, Modifying, and Saving Instrument SettingsVoyager™ Biospectrometry™ Workstation User’s Guide 5-55Table 5-2 Reflector Mode .BIC Files.BIC Fil

Chapter 5 Optimizing Instrument Settings5-6 PerSeptive Biosystems5NOTE: For CID applications, use Substance_P_Precursor.BIC method with the approp

Loading, Modifying, and Saving Instrument SettingsVoyager™ Biospectrometry™ Workstation User’s Guide 5-755.1.3 Opening and Viewing Instrument Setting

Chapter 5 Optimizing Instrument Settings5-8 PerSeptive Biosystems5Opening from .DATTo open an instrument settings file from a .DAT file, select .D

Loading, Modifying, and Saving Instrument SettingsVoyager™ Biospectrometry™ Workstation User’s Guide 5-95Modifying forManual ControlmodeTo modify the

Safety and Compliance Informationxxiv PerSeptive Biosystems1Canadian Safetyand EMCStandardsSafetyThis instrument has been tested to and complies with

Chapter 5 Optimizing Instrument Settings5-10 PerSeptive Biosystems53. Select Manual Control mode. For parameter descriptions, see Section 5.2.1, I

Loading, Modifying, and Saving Instrument SettingsVoyager™ Biospectrometry™ Workstation User’s Guide 5-1155.1.5 Saving and Printing Instrument Settin

Chapter 5 Optimizing Instrument Settings5-12 PerSeptive Biosystems5Saving .BIC filesfor differentmodesWhen saving .BIC files for use in different

Loading, Modifying, and Saving Instrument SettingsVoyager™ Biospectrometry™ Workstation User’s Guide 5-1355.1.6 Setting Instrument Settings Files to

Chapter 5 Optimizing Instrument Settings5-14 PerSeptive Biosystems55.2 Instrument Settings Parameter DescriptionsThis section describes the param

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-1555.2.1 Instrument Settings PageSelect Instrument Set

Chapter 5 Optimizing Instrument Settings5-16 PerSeptive Biosystems5Instrument settings parameters are described in Table 5-4.Table 5-4 Instrumen

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-175VoltagesAccelerating Voltage Voltage applied to the

Chapter 5 Optimizing Instrument Settings5-18 PerSeptive Biosystems5Guide Wire Voltage% Voltage applied to the beam guide wire. Overcomes the dispe

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-195Shots/Spectrum Determines the number of laser shots

Safety and Compliance InformationVoyager™ Biospectrometry™ Workstation User’s Guide xxv1Laser SafetyLaserclassificationThe Voyager™ Biospectrometry™ W

Chapter 5 Optimizing Instrument Settings5-20 PerSeptive Biosystems5Spectrum Acquisition (continued)Low Mass Gate (Da) Turns on the detector voltag

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-215Calibration (continued)Default Enables default calib

Chapter 5 Optimizing Instrument Settings5-22 PerSeptive Biosystems5Matrix influenceThe initial velocity is the average speed at which matrix ions

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-235Modifying thematrix referencefileMatrix options are

Chapter 5 Optimizing Instrument Settings5-24 PerSeptive Biosystems55.2.2 Mode/Digitizer Settings Dialog BoxClick Mode/Digitizer Settings in the I

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-255Instrument ModeparametersClick the Instrument Mode t

Chapter 5 Optimizing Instrument Settings5-26 PerSeptive Biosystems5Linear/ReflectorDigitizerparametersClick the Linear or Reflector Digitizer tab

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-275 Table 5-7 Linear and Reflector Digitizer Paramete

Chapter 5 Optimizing Instrument Settings5-28 PerSeptive Biosystems5Vertical SettingsVertical Scale Specifies the input range of the digitizer in m

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-295AdvancedparametersClick the Advanced tab to display

Safety and Compliance Informationxxvi PerSeptive Biosystems1

Chapter 5 Optimizing Instrument Settings5-30 PerSeptive Biosystems5Table 5-8 Advanced ParametersParameter DescriptionMirror to Accelerating Volt

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-3155.2.3 Automatic Control Dialog BoxOn the Instrument

Chapter 5 Optimizing Instrument Settings5-32 PerSeptive Biosystems5For information on setting Instrument Settings for Automatic Control mode, see

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-335Table 5-10 Automatic Control Parameters—Spectrum A

Chapter 5 Optimizing Instrument Settings5-34 PerSeptive Biosystems5Save Conditions(continued)• Save all spectra that pass acceptance criteria— Eac

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-355Save Conditions(continued)• Save first spectrum to p

Chapter 5 Optimizing Instrument Settings5-36 PerSeptive Biosystems5Accumulation ConditionsThe following Accumulation conditions create one data fi

Instrument Settings Parameter DescriptionsVoyager™ Biospectrometry™ Workstation User’s Guide 5-375Accumulation Conditions(continued)Accumulate all pas

Chapter 5 Optimizing Instrument Settings5-38 PerSeptive Biosystems5Table 5-11 Automatic Control Parameters—Sample PositioningParameter Descripti

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-3955.3 Impact of Changing Instrument Settings P

How to Use This GuideVoyager Biospectrometry Workstation User’s Guide xxvii1How to Use This GuidePurpose of thisguidePerSeptive Biosystems’ Voyager Bi

Chapter 5 Optimizing Instrument Settings5-40 PerSeptive Biosystems5Grid Voltage% Linear/ ReflectorCritical parameter with optimum value for maximu

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-4155.3.2 Understanding Grid Voltage%NOTE: You m

Chapter 5 Optimizing Instrument Settings5-42 PerSeptive Biosystems5Potential gradientThe potential gradient in the ionization region (Figure 5-8)

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-435For example (Figure 5-8), with a 25,000 V Acc

Chapter 5 Optimizing Instrument Settings5-44 PerSeptive Biosystems55.3.3 Understanding Delay TimeDelay Time is the time in nanoseconds after the

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-455Relationship toGrid Voltage%Delay Time and Gr

Chapter 5 Optimizing Instrument Settings5-46 PerSeptive Biosystems55.3.4 Understanding Guide Wire Voltage%By applying voltage to the beam guide w

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-475Reflector mode• To obtain maximum resolution

Chapter 5 Optimizing Instrument Settings5-48 PerSeptive Biosystems5Default Number ofData Points/BinSize settingsThe software uses the following de

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-495Effects ofadjusting Bin sizeA smaller Bin siz

How to Use This Guidexxviii PerSeptive Biosystems1Chapter 6, Acquiring Mass SpectraDescribes how to use the Voyager processing software, including lab

Chapter 5 Optimizing Instrument Settings5-50 PerSeptive Biosystems55.3.5.2 Vertical Digitizer SettingsThis section describes:• Vertical settings•

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-515Figure 5-12 Effect of Vertical Scale in Digi

Chapter 5 Optimizing Instrument Settings5-52 PerSeptive Biosystems5When to increaseIncrease the Vertical Scale if signal goes offscale (Figure 5-1

Impact of Changing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-535Input Bandwidth(not available withSignatecdig

Chapter 5 Optimizing Instrument Settings5-54 PerSeptive Biosystems55.4 Optimizing Instrument Settings ParametersIn this sectionThis section descr

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-5555.4.1 Optimization StrategyThis section gives a sugg

Chapter 5 Optimizing Instrument Settings5-56 PerSeptive Biosystems5StrategyTo optimize instrument settings, do the following:1. Open a .BIC file f

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-5755.4.2 Determining the Laser SettingThis section incl

Chapter 5 Optimizing Instrument Settings5-58 PerSeptive Biosystems5Adjusting laserintensityTo efficiently optimize the laser setting, increase or

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-595• If the spectrum you obtain is not acceptable, incre

How to Use This GuideVoyager Biospectrometry Workstation User’s Guide xxix1RelateddocumentationThese related documents are shipped with your system:•V

Chapter 5 Optimizing Instrument Settings5-60 PerSeptive Biosystems5NOTE: Saturated signal in any region of the spectrum may suppress peaks in the

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-6155.4.3 Optimizing ResolutionThis section includes:•Ov

Chapter 5 Optimizing Instrument Settings5-62 PerSeptive Biosystems55.4.3.1 OverviewThis section includes:• Parameters to adjust•DE parameters • R

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-635DE parametersImproved resolution in Delayed Extractio

Chapter 5 Optimizing Instrument Settings5-64 PerSeptive Biosystems5Effects of massand matrixNote the following:• At a fixed Delay Time, higher mas

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-6555.4.3.2 Acceptable Resolution in Delayed Extraction

Chapter 5 Optimizing Instrument Settings5-66 PerSeptive Biosystems5If you cannot obtain the resolution listed for the mass range of interest, cons

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-6755.4.3.4 Optimizing Delay TimeThis section includes:•

Chapter 5 Optimizing Instrument Settings5-68 PerSeptive Biosystems5Optimizing DelayTimeNOTE: If you are analyzing a broad mass range and need opti

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-6953. If the resolution improves by at least 20 percent

Table of ContentsVoyager Biospectrometry Workstation User’s Guide iiiTable of ContentsSafety and Compliance Information ...

How to Use This Guidexxx PerSeptive Biosystems1You also receive the appropriate manual for the digitizer included with your system:• Signatec Digitize

Chapter 5 Optimizing Instrument Settings5-70 PerSeptive Biosystems5NOTE: Changing the Delay Time in increments smaller than 25 nsec may have no si

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-7154. Continue increasing (or decreasing) the Delay Time

Chapter 5 Optimizing Instrument Settings5-72 PerSeptive Biosystems55.4.3.5 Optimizing Grid Voltage%OverviewYou can use this procedure as an alter

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-735Optimizing GridVoltage%To optimize Grid Voltage%:1. O

Chapter 5 Optimizing Instrument Settings5-74 PerSeptive Biosystems5If the resolution does not improve, decrease the Grid Voltage% (by 0.5 percent

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-7555.4.4 Optimizing Signal-to-Noise RatioThis section i

Chapter 5 Optimizing Instrument Settings5-76 PerSeptive Biosystems55.4.4.1 OverviewYou can set the following parameters to optimize signal-to-noi

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-7755.4.4.2 Setting Accelerating VoltageOverviewAccelera

Chapter 5 Optimizing Instrument Settings5-78 PerSeptive Biosystems5A lower Accelerating Voltage setting does the following:• Provides more data po

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-7955.4.4.4 Setting Shots/SpectrumOverviewA higher numbe

1ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 1-11 Introducing theVoyager™Biospectrometry™WorkstationsThis chapter contains the followin

Chapter 5 Optimizing Instrument Settings5-80 PerSeptive Biosystems5When to useTurn on Low Mass Gate when:• Analyzing masses greater than 2,000–3,0

Optimizing Instrument Settings ParametersVoyager™ Biospectrometry™ Workstation User’s Guide 5-815Figure 5-20 Low Mass Gate Spike The spike occurs at

Chapter 5 Optimizing Instrument Settings5-82 PerSeptive Biosystems5

6ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 6-16 Acquiring Mass SpectraThis chapter contains the following sections:6.1 Before You Be

Chapter 6 Acquiring Mass Spectra6-2 PerSeptive Biosystems66.1 Before You BeginThis section includes:• Overview of acquisition options• Guidelines

Before You BeginVoyager™ Biospectrometry™ Workstation User’s Guide 6-36Automatic Control mode in Instrument Control Panel• Single sample• Automatic/ma

Chapter 6 Acquiring Mass Spectra6-4 PerSeptive Biosystems66.1.2 Guidelines for AcquiringThis section includes:• High voltage warmup for improved

Before You BeginVoyager™ Biospectrometry™ Workstation User’s Guide 6-56When acquiring aspectrumWhen acquiring a spectrum, note the following:• For the

Chapter 6 Acquiring Mass Spectra6-6 PerSeptive Biosystems6• Observe the Spectrum window or Oscilloscope screen to determine if data is acceptable.

Before You BeginVoyager™ Biospectrometry™ Workstation User’s Guide 6-766.1.3 Calibrating the Mass ScaleThis section describes:• Types of calibration•

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-2 PerSeptive Biosystems11.1 Voyager™-DE and Voyager-DE PRO System OverviewThe

Chapter 6 Acquiring Mass Spectra6-8 PerSeptive Biosystems6• Sequence Control calibration–Provides external, internal, and internal with automatic

Before You BeginVoyager™ Biospectrometry™ Workstation User’s Guide 6-96CalibrationequationsThe general equation that the Voyager software uses for cal

Chapter 6 Acquiring Mass Spectra6-10 PerSeptive Biosystems6GeneratedcalibrationIf you are performing an internal standard calibration, the softwar

Acquiring in Manual Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-1166.2 Acquiring in Manual Mode from t

Chapter 6 Acquiring Mass Spectra6-12 PerSeptive Biosystems6Figure 6-2 Instrument Control Panel Before AcquiringNOTE: If the Instrument Settings c

Acquiring in Manual Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-1363. Specify calibration information:•

Chapter 6 Acquiring Mass Spectra6-14 PerSeptive Biosystems6Hint: You can double-click on the control page to “undock” it, and click-drag it to any

Acquiring in Manual Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-1563. Type a filename.4. Select Autoseq

Chapter 6 Acquiring Mass Spectra6-16 PerSeptive Biosystems6DuringacquisitionDuring acquisition:• The Live/Current Spectrum trace in the Spectrum w

Acquiring in Manual Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-176Figure 6-4 Checking for Signal Satu

Voyager™-DE and Voyager-DE PRO System OverviewVoyager™ Biospectrometry™ Workstation User’s Guide 1-31Voyager-DE PROThe Voyager-DE™PRO Biospectrometry™

Chapter 6 Acquiring Mass Spectra6-18 PerSeptive Biosystems6Saving dataTo save the data when you have more than one trace displayed in the Spectrum

Acquiring in Manual Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-1966.2.2 Manually Accumulating Spectra

Chapter 6 Acquiring Mass Spectra6-20 PerSeptive Biosystems66.3 Obtaining Good Spectra in Delayed Extraction ModeThis section describes:• What is

Obtaining Good Spectra in Delayed Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide 6-216Figure 6-6 Example of Poor Mass Spectrum for

Chapter 6 Acquiring Mass Spectra6-22 PerSeptive Biosystems6Figure 6-8 Example of Poor Mass Spectrum for AngiotensinFigure 6-9 Example of Good Ma

Obtaining Good Spectra in Delayed Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide 6-2366.3.2 Laser IntensityOverviewLaser intensity

Chapter 6 Acquiring Mass Spectra6-24 PerSeptive Biosystems6Prompt fragmentsPrompt fragments appear in the spectrum at masses that correspond to th

Making Accurate Mass MeasurementsVoyager™ Biospectrometry™ Workstation User’s Guide 6-2566.4 Making Accurate Mass MeasurementsOverviewAccurate mass m

Chapter 6 Acquiring Mass Spectra6-26 PerSeptive Biosystems6• Signal intensity of reference and analyte peaks is in the same range—Signal intensity

Evaluating Data in the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-2766.5 Evaluating Data in the Instrument Control

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-4 PerSeptive Biosystems1FeaturesFeatures of the Voyager-DE and Voyager-DE PRO

Chapter 6 Acquiring Mass Spectra6-28 PerSeptive Biosystems6NOTE: The parameters in this dialog box correspond to the Advanced Settings tab in the

Evaluating Data in the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-2966.5.2 Calculating Mass ResolutionYou can calcu

Chapter 6 Acquiring Mass Spectra6-30 PerSeptive Biosystems65. Type in up to four Mass/Charge values for which to calculate resolution.6. For each

Evaluating Data in the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-316Figure 6-13 Resolution Calculator ResultsThe t

Chapter 6 Acquiring Mass Spectra6-32 PerSeptive Biosystems66.5.3 Calculating Signal-to-RMS Noise Ratio OverviewA signal-to-RMS noise ratio is typ

Evaluating Data in the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-3364. For each Mass/Charge, enter the window for c

Chapter 6 Acquiring Mass Spectra6-34 PerSeptive Biosystems66.6 Acquiring in Automatic Mode from the Instrument Control PanelThis section includes

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-356See Section 2.7, Aligning the Sam

Chapter 6 Acquiring Mass Spectra6-36 PerSeptive Biosystems6NOTE: Make sure the instrument settings yield acceptable results in Manual Control mode

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-376Laser4. Select Use Automated Lase

Voyager-DE STR System OverviewVoyager™ Biospectrometry™ Workstation User’s Guide 1-511.2 Voyager-DE STR System OverviewVoyager-DE STRThe Voyager™-DE

Chapter 6 Acquiring Mass Spectra6-38 PerSeptive Biosystems6Spectrumaccumulation andsaving8. Specify Spectrum Accumulation parameters:• Acquire X S

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-396Sample positioning10. Select Use

Chapter 6 Acquiring Mass Spectra6-40 PerSeptive Biosystems6Setting spectrumacceptance andlaser adjustmentcriteriaIf you selected an accumulation c

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-416Table 6-3 Spectrum Acceptance C

Chapter 6 Acquiring Mass Spectra6-42 PerSeptive Biosystems63. Click OK to close the Spectrum Acceptance Criteria dialog box.4. Click OK to close t

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-4366.6.3 Automatically Acquiring, E

Chapter 6 Acquiring Mass Spectra6-44 PerSeptive Biosystems6DuringacquisitionDuring acquisition:• Laser is adjusted, sample position is adjusted, a

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-456A search pattern file is an ASCII

Chapter 6 Acquiring Mass Spectra6-46 PerSeptive Biosystems6Default searchpattern fileThe default search pattern file for a 100-position plate (DEF

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-476Spiral searchpattern fileThe SPIR

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-6 PerSeptive Biosystems1BiospectrometryBiospectrometry is the application of m

Chapter 6 Acquiring Mass Spectra6-48 PerSeptive Biosystems6Hint: To determine coordinates, spot a sample plate with standard, load the plate, star

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-4966.6.5 Process that Occurs During

Chapter 6 Acquiring Mass Spectra6-50 PerSeptive Biosystems6In Prescan mode, the system does the following:1. The system sets the laser to the maxi

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-5162. The system sets the laser to t

Chapter 6 Acquiring Mass Spectra6-52 PerSeptive Biosystems6Acquisition modeAcquisition mode starts after Prescan mode determines the laser setting

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-536NOTE: If no minimum or maximum si

Chapter 6 Acquiring Mass Spectra6-54 PerSeptive Biosystems64. If Save All or Accumulate All is selected for accumulation, the system moves to the

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-556If Acceptance Criteria are not me

Chapter 6 Acquiring Mass Spectra6-56 PerSeptive Biosystems66.6.6 Process that Occurs when Accumulating Spectra from Multiple Search Pattern Posit

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-5766.6.6.1 Process that Occurs when

MALDI-TOF MS Technology OverviewVoyager™ Biospectrometry™ Workstation User’s Guide 1-711.3 MALDI-TOF MS Technology OverviewMassspectrometryMass spect

Chapter 6 Acquiring Mass Spectra6-58 PerSeptive Biosystems66.6.6.2 Process that Occurs when Accumulating Passing SpectraWhen accumulating only th

Acquiring in Automatic Mode from the Instrument Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-5969. Repeats step 2 through step 8

Chapter 6 Acquiring Mass Spectra6-60 PerSeptive Biosystems66.7 Acquiring Spectra from the Sequence Control PanelOverviewThe Voyager Sequence Cont

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-616Figure 6-19 Sequence Control Panel

Chapter 6 Acquiring Mass Spectra6-62 PerSeptive Biosystems66.7.1 Understanding Settings, Macros, and CalibrationThis section includes:• File type

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-636How file typesand calibrationspecified affect

Chapter 6 Acquiring Mass Spectra6-64 PerSeptive Biosystems6Figure 6-20 Settings, Macros, and Calibration in Sequence ControlNoCalibrationDataExte

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-6566.7.2 Before Creating a SequenceThis section

Chapter 6 Acquiring Mass Spectra6-66 PerSeptive Biosystems6Creating macrosYou can specify macros that execute before and after calibration. You ca

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-676Creating settings(.SET) filesCreate settings

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-8 PerSeptive Biosystems1Matrix-AssistedLaser DesorptionIonization (MALDI)In Ma

Chapter 6 Acquiring Mass Spectra6-68 PerSeptive Biosystems66.7.3.1 Setting General Sequence ParametersSet parameters as needed:1. From the View m

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-696NOTE: Run logs are overwritten each time you

Chapter 6 Acquiring Mass Spectra6-70 PerSeptive Biosystems6Figure 6-22 Sequence Run ListHint: You can show and hide columns by selecting a column

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-716Instrument Settings File(required entry) .BIC

Chapter 6 Acquiring Mass Spectra6-72 PerSeptive Biosystems6Internal/External CalibrationCalibration type to use for this row. Click the down arrow

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-736Calibration File(required entry for External,

Chapter 6 Acquiring Mass Spectra6-74 PerSeptive Biosystems65. When all necessary rows are filled in, save the sequence by selecting Save Sequence

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-756Modifying andcustomizing therun listYou can m

Chapter 6 Acquiring Mass Spectra6-76 PerSeptive Biosystems6ImportingTo import a .TXT or .XLS file:1. Select Import from the File menu.2. Select a

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-7766.7.4 Preparing to Run a SequenceThis sectio

MALDI-TOF MS Technology OverviewVoyager™ Biospectrometry™ Workstation User’s Guide 1-91For acquiring TOF spectra, time measurement starts:• Delayed Ex

Chapter 6 Acquiring Mass Spectra6-78 PerSeptive Biosystems6Before acquiringBefore acquiring a sequence:1. Load a sequence by doing one of the foll

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-796Pausing andresuming asequenceTo pause a seque

Chapter 6 Acquiring Mass Spectra6-80 PerSeptive Biosystems66.7.6 Checking Sequence StatusYou can check sequence status in three places:• Acquisit

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-816Sequence status parameters include:Checking s

Chapter 6 Acquiring Mass Spectra6-82 PerSeptive Biosystems66.7.7 Automatic Calibration During a Sequence RunThis section includes:• Calibration o

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-8366.7.7.2 Calibration Standard RequirementsMas

Chapter 6 Acquiring Mass Spectra6-84 PerSeptive Biosystems6Sample andstandard inseparate samplepositionsIf you are acquiring samples and standards

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-856The number and placement of standards needed

Chapter 6 Acquiring Mass Spectra6-86 PerSeptive Biosystems6To acquire sample and standard, create two search pattern files to analyze the sample a

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-876NOTE: Use plates without laser-etched sample

Table of Contentsiv PerSeptive BiosystemsChapter 2 Installing the Voyager™ Biospectrometry™ Workstations2.1 Installing the System ...

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-10 PerSeptive Biosystems1Drift time is proportional to the square root of the

Chapter 6 Acquiring Mass Spectra6-88 PerSeptive Biosystems6If standard signal suppresses unknown signal, you have two options for analysis:• Perfo

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-8962. Load the sample plate, select the position

Chapter 6 Acquiring Mass Spectra6-90 PerSeptive Biosystems66.7.8 Customizing the Sequence DisplayUsing WorkbookmodeWorkbook mode displays the run

Acquiring Spectra from the Sequence Control PanelVoyager™ Biospectrometry™ Workstation User’s Guide 6-9165. To set preferences, select Preferences fro

Chapter 6 Acquiring Mass Spectra6-92 PerSeptive Biosystems6

7ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 7-17 PSD AnalysisThis chapter contains the following sections:7.1 Overview of PSD Analysi

Chapter 7 PSD Analysis7-2 PerSeptive Biosystems77.1 Overview of PSD AnalysisThis section includes:• Post-source decay analysis• Segments and comp

Overview of PSD AnalysisVoyager™ Biospectrometry™ Workstation User’s Guide 7-37PSD fragmentionsAt higher laser intensities, some molecular ions decomp

Chapter 7 PSD Analysis7-4 PerSeptive Biosystems7Figure 7-1 Molecular and Fragment Ion Flight in the ReflectorThe AH+ fragment has 70 percent of t

Overview of PSD AnalysisVoyager™ Biospectrometry™ Workstation User’s Guide 7-57Figure 7-2 Effect of Changing Mirror RatioA Mirror Ratio setting of 1.

Voyager-DE™ (Delayed Extraction™) TechnologyVoyager™ Biospectrometry™ Workstation User’s Guide 1-1111.4 Voyager-DE™ (Delayed Extraction™) TechnologyI

Chapter 7 PSD Analysis7-6 PerSeptive Biosystems77.1.2 Segments and Composite SpectraOverviewTo obtain the most information about an ion, collect

Overview of PSD AnalysisVoyager™ Biospectrometry™ Workstation User’s Guide 7-777.1.3 PSD Data FilesPSD data (.DAT) files include:• Precursor ion mass

Chapter 7 PSD Analysis7-8 PerSeptive Biosystems77.1.4 Mass Calculation for Fragment IonsPSD calibrationequationPSD calibration specifies the mass

Overview of PSD AnalysisVoyager™ Biospectrometry™ Workstation User’s Guide 7-977.1.5 Optimizing the Precursor Ion SelectorThe Precursor Ion Selector

Chapter 7 PSD Analysis7-10 PerSeptive Biosystems7Figure 7-4 Timed Ion Selector Tab in Hardware Configuration Dialog BoxSet the Deflector Gate Wid

Enhancing Fragmentation with CIDVoyager™ Biospectrometry™ Workstation User’s Guide 7-1177.2 Enhancing Fragmentation with CIDOverviewCollision-induced

Chapter 7 PSD Analysis7-12 PerSeptive Biosystems7BenefitsThe benefits provided by CID include: • Fragmentation of ions that does not occur under n

Enhancing Fragmentation with CIDVoyager™ Biospectrometry™ Workstation User’s Guide 7-137Figure 7-7 Mid Masses—Impact of CID (Glu-1-Fibrinopeptide)In

Chapter 7 PSD Analysis7-14 PerSeptive Biosystems7Purging collisiongas linesBefore turning on the collision gas, purge the lines to prevent disrupt

Enhancing Fragmentation with CIDVoyager™ Biospectrometry™ Workstation User’s Guide 7-157Turning oncollision gasTo turn on the collision gas after purg

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-12 PerSeptive Biosystems1DelayedExtractionWith Voyager-DE™ (Delayed Extraction

Chapter 7 PSD Analysis7-16 PerSeptive Biosystems7Turning offcollision gasTo turn off the collision gas:1. Turn the top 3-way valve on the CID box

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-1777.3 Acquiring PSD Data with

Chapter 7 PSD Analysis7-18 PerSeptive Biosystems7Differences fromregular analysisWhen operating in PSD mode, note the following differences from a

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-1977.3.1 Determining the Precur

Chapter 7 PSD Analysis7-20 PerSeptive Biosystems7Generating anexternalcalibration for theprecursor ionTo obtain maximum mass accuracy for the prec

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-2177.3.2 Determining the Number

Chapter 7 PSD Analysis7-22 PerSeptive Biosystems7Hint: You can use the Windows calculator to determine natural log values. If the ln function is n

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-237Size of segmentsYou can acqui

Chapter 7 PSD Analysis7-24 PerSeptive Biosystems77.3.3 Setting PSD Acquisition ParametersSetting PSD Acquisition parameters includes:• Displaying

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-2572. If the PSD Acquisition Set

Voyager-DE™ (Delayed Extraction™) TechnologyVoyager™ Biospectrometry™ Workstation User’s Guide 1-131In Continuous Extraction mode:• Accelerating volta

Chapter 7 PSD Analysis7-26 PerSeptive Biosystems74. In the Calibration section of the Instrument Settings control page, select the matrix you are

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-277NOTE: The calibration you spe

Chapter 7 PSD Analysis7-28 PerSeptive Biosystems77.3.4 Filling in the Segment List This section describes:• Filling in the list• Typing or select

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-297Rows are added with the follo

Chapter 7 PSD Analysis7-30 PerSeptive Biosystems7Typing orselecting newvaluesTo type or select new values in the segment list:1. Type in new value

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-317NOTE: Do not select Guide Wir

Chapter 7 PSD Analysis7-32 PerSeptive Biosystems77.3.5 Acquiring and Saving PSD SegmentsThis section includes:•Overview• Acquiring PSD segments•

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-337NOTE: If you stop an experime

Chapter 7 PSD Analysis7-34 PerSeptive Biosystems7DuringacquisitionThe following occurs:• Mass range for the segment is set to:• Acquisition starts

Acquiring PSD Data with Standard Instrument Settings (.BIC) FilesVoyager™ Biospectrometry™ Workstation User’s Guide 7-357Accumulating orsaving thesegm

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-14 PerSeptive Biosystems1Benefits ofDelayedExtractionDelayed Extraction of ion

Chapter 7 PSD Analysis7-36 PerSeptive Biosystems77.4 Exploring PSD ModeTo be successful in PSD analysis, you need to understand how ions behave i

Exploring PSD ModeVoyager™ Biospectrometry™ Workstation User’s Guide 7-3777.4.1 Observing the Effects of Laser IntensityAdjusting laser intensity aff

Chapter 7 PSD Analysis7-38 PerSeptive Biosystems75. Note the behavior of the signal intensity for the first few spectra and subsequent continued s

Exploring PSD ModeVoyager™ Biospectrometry™ Workstation User’s Guide 7-397Hint: As you initially experiment, adjust the laser in large steps, for exam

Chapter 7 PSD Analysis7-40 PerSeptive Biosystems77.4.2 Observing the Effects of Precursor Ion SelectorTurning on the Precursor Ion Selector elimi

Exploring PSD ModeVoyager™ Biospectrometry™ Workstation User’s Guide 7-417Figure 7-12 compares the spectrum above with the spectrum acquired in the pr

Chapter 7 PSD Analysis7-42 PerSeptive Biosystems7Observing promptand PSDfragmentsWhen operating under conditions that yield high resolution for an

Exploring PSD ModeVoyager™ Biospectrometry™ Workstation User’s Guide 7-437Figure 7-13 Flight Path of Prompt and PSD FragmentsPath of prompt fragment

Chapter 7 PSD Analysis7-44 PerSeptive Biosystems77.4.3 Observing the Effects of Grid Voltage% Adjusting Grid Voltage% affects resolution.In this

Exploring PSD ModeVoyager™ Biospectrometry™ Workstation User’s Guide 7-457By fine-tuning the Grid Voltage%, you can alter the point of initial time fo

Voyager-DE™ (Delayed Extraction™) TechnologyVoyager™ Biospectrometry™ Workstation User’s Guide 1-151Velocity focusingDelayed Extraction technology fac

Chapter 7 PSD Analysis7-46 PerSeptive Biosystems7AcquiringNOTE: In this exercise, you will observe the impact of the Grid Voltage% on the precurso

Exploring PSD ModeVoyager™ Biospectrometry™ Workstation User’s Guide 7-4776. Check the Grid Voltage% setting in the standard .BIC file provided on you

Chapter 7 PSD Analysis7-48 PerSeptive Biosystems77.5 Viewing PSD DataFor information on viewing PSD data, see the Data Explorer Software User’s G

8ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 8-138 Maintenance andTroubleshootingThis chapter contains the following sections:8.1 Main

Chapter 8 Maintenance and Troubleshooting8-2 PerSeptive Biosystems88.1 MaintenanceThis section describes:• Maintenance schedule• Hardware mainten

MaintenanceVoyager™ Biospectrometry™ Workstation User’s Guide 8-388.1.2 Hardware MaintenanceWARNINGELECTRICAL SHOCK HAZARD. Severe electrical shock c

Chapter 8 Maintenance and Troubleshooting8-4 PerSeptive Biosystems8• Inspect flap valve 1, flap valve 2, linear actuator o-rings• Clean optics and

MaintenanceVoyager™ Biospectrometry™ Workstation User’s Guide 8-58Figure 8-1 Changing FusesWARNINGFIRE HAZARD. Using a fuse of the wrong type or rati

Chapter 8 Maintenance and Troubleshooting8-6 PerSeptive Biosystems86. Insert two fuses of the proper rating.7. Insert the voltage selector/fuse ho

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-788.2 TroubleshootingThis section includes:• Spectrum troubleshooting• Software t

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-16 PerSeptive Biosystems1Figure 1-10 Velocity Focusing of Ions in Linear Mode

Chapter 8 Maintenance and Troubleshooting8-8 PerSeptive Biosystems8Flat signal on oscilloscope or in spectrum window for sample region (matrix pea

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-98Flat signal on oscilloscope or in spectrum window for sample and matrix regionVe

Chapter 8 Maintenance and Troubleshooting8-10 PerSeptive Biosystems8Poor resolution/ sensitivity in Delayed Extraction modeDelay Time and Grid Vol

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-118Round tops on peaks Saturated (flat top) and unsaturated (sharp top) scans aver

Chapter 8 Maintenance and Troubleshooting8-12 PerSeptive Biosystems8Poor mass accuracy in Delayed Extraction mode(external calibration only)High v

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-138Poor signal-to-noise ratio or sensitivity(continued on next page)Laser intensit

Chapter 8 Maintenance and Troubleshooting8-14 PerSeptive Biosystems8Poor signal-to-noise ratio or sensitivity(continued)Guide Wire Voltage% too hi

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-158Dimer in spectrum Laser intensity too highAdjust laser by using the slider cont

Chapter 8 Maintenance and Troubleshooting8-16 PerSeptive Biosystems8Peaks not symmetrical Laser intensity too high Decrease laser intensity by usi

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-178On Voyager-DE PRO and Voyager-DE STR systems, cannot see high mass ions in Refl

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-1711.5 Parts of the Voyager-DE andVoyager-DE P

Chapter 8 Maintenance and Troubleshooting8-18 PerSeptive Biosystems8Large tail on the high mass side of peakUnresolved salt or buffer adducts due

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-1988.2.2 Software TroubleshootingThis section includes:• Instrument Control Panel

Chapter 8 Maintenance and Troubleshooting8-20 PerSeptive Biosystems8Calibration (mass) shifted up or down by 10 Da Uneven matrix layer causing hot

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-218Checking theWindows NTEvent LogThe Windows NT Event Log is a running list of ev

Chapter 8 Maintenance and Troubleshooting8-22 PerSeptive Biosystems88.2.3 Hardware TroubleshootingThis section includes:• Mass spectrometer troub

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-238Cracking sound in mass spectrometerArcing caused by dirty sample plateUse clean

Chapter 8 Maintenance and Troubleshooting8-24 PerSeptive Biosystems8Sample holder empty when you click EjectSample plate too far way from grabber

TroubleshootingVoyager™ Biospectrometry™ Workstation User’s Guide 8-258E09 error message displayed on gauge controller for BA1 or BA2BA1 or BA2 gauges

Chapter 8 Maintenance and Troubleshooting8-26 PerSeptive Biosystems8

AAppendixVoyager™ Biospectrometry™ Workstation User’s Guide A-1A SpecificationsThis appendix contains the following sections:A.1 Voyager-DE Specific

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-18 PerSeptive Biosystems1Voyager-DE PROThe Voyager-DE PRO Biospectrometry Work

Appendix A SpecificationsA-2 PerSeptive BiosystemsAA.1 Voyager-DE SpecificationsThis section includes the following specifications for the Voyage

Voyager-DE SpecificationsVoyager™ Biospectrometry™ Workstation User’s Guide A-3AIon source voltages Tunable:• Accelerating Voltage—Up to 25,000 V• Gri

Appendix A SpecificationsA-4 PerSeptive BiosystemsAA.2 Voyager-DE PRO SpecificationsThis section includes the following specifications for the Vo

Voyager-DE PRO SpecificationsVoyager™ Biospectrometry™ Workstation User’s Guide A-5ATable A-5 Voyager-DE PRO Mass Spectrometer SpecificationsConditi

Appendix A SpecificationsA-6 PerSeptive BiosystemsATable A-6 Voyager-DE PRO Miscellaneous SpecificationsCondition SpecificationOperating tempera

Voyager-DE STR SpecificationsVoyager™ Biospectrometry™ Workstation User’s Guide A-7AA.3 Voyager-DE STR SpecificationsThis section includes the follow

Appendix A SpecificationsA-8 PerSeptive BiosystemsATable A-8 Voyager-DE STR Mass Spectrometer SpecificationsCondition SpecificationReflector Sin

Voyager-DE STR SpecificationsVoyager™ Biospectrometry™ Workstation User’s Guide A-9ATable A-9 Voyager-DE STR Miscellaneous SpecificationsCondition S

Appendix A SpecificationsA-10 PerSeptive BiosystemsA

BAppendixVoyager™ Biospectrometry™ Workstation User’s Guide B-1B Warranty/ServiceInformationThis appendix contains the following sections:B.1 Limite

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-191Parts of the Voyager-DE and Voyager-DE PRO s

Appendix B Warranty/Service InformationB-2 PerSeptive BiosystemsBB.1 Limited Product WarrantyLimited warrantyPerSeptive Biosystems, Inc. (“PerSep

Voyager™ Biospectrometry™ Workstation User’s Guide B-3BPerSeptive warrants that for a period of ninety (90) days the software designated for use with

Appendix B Warranty/Service InformationB-4 PerSeptive BiosystemsBWarrantylimitationsTHE REMEDIES PROVIDED HEREIN ARE BUYER’S SOLE AND EXCLUSIVE RE

Voyager™ Biospectrometry™ Workstation User’s Guide B-5BB.2 Damages, Claims, ReturnsDamagesPlease examine any shipments promptly after receipt to chec

Appendix B Warranty/Service InformationB-6 PerSeptive BiosystemsBB.3 Spare PartsStandards andmatricesThe following compounds are available from t

Voyager™ Biospectrometry™ Workstation User’s Guide B-7BSample platesThe following sample plates are available from PerSeptive Biosystems:Description P

Appendix B Warranty/Service InformationB-8 PerSeptive BiosystemsBMembrane, Gels V700698Hydrophobic plastic surface, flat, 400-position V700699Desc

CAppendixVoyager™ Biospectrometry™ Workstation User’s Guide C-1C MatricesThis appendix lists commonly used matrices. For each matrix, it also lists:•

Appendix C MatricesC-2 PerSeptive BiosystemsCFigure C-1 Sinapinic Acid Matrix SpectrumFigure C-2 α-cyano-4-hydroxycinnamic acid (CHCA) Matrix Sp

Voyager™ Biospectrometry™ Workstation User’s Guide C-3CFigure C-3 2,5-dihydroxybenzoic acid (2,5-DHB) Matrix SpectrumFigure C-4 Mixture of 2,5-dihyd

Table of ContentsVoyager Biospectrometry Workstation User’s Guide vChapter 3 Preparing Samples3.1 Preparing Samples ...

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-20 PerSeptive Biosystems11.5.2 Mass SpectrometerVoyager-DEThe parts of the Vo

Appendix C MatricesC-4 PerSeptive BiosystemsCFigure C-5 2-(4-hydroxy-phenylazo)-benzoic acid (HABA) Matrix SpectrumFigure C-6 3-hydroxypicolinic

Voyager™ Biospectrometry™ Workstation User’s Guide C-5CFigure C-7 Dithranol Matrix SpectrumFigure C-8 2,4,6 trihydroxyacetophenone (THAP) Spectrum

Appendix C MatricesC-6 PerSeptive BiosystemsCFigure C-9 trans-3-indoleacrylic acid (IAA) Matrix SpectrumMatrix Applications/ColorMatrix Solution

Voyager™ Biospectrometry™ Workstation User’s Guide C-7CAlpha-cyano-4-hydroxycinnamic acid (αCHCA)(see mass spectrum on page C-2)MW 189.04 DaApplicatio

Appendix C MatricesC-8 PerSeptive BiosystemsC2,5-dihydroxybenzoic acid (2,5-DHB)(see mass spectrum on page C-3)MW 154.03 DaApplications:Small mole

Voyager™ Biospectrometry™ Workstation User’s Guide C-9Cmixture of 2,5-dihydroxybenzoic acid and 5-methoxysalicylic acid (DHBs)(see mass spectrum on pa

Appendix C MatricesC-10 PerSeptive BiosystemsC2-(4-hydroxy-phenylazo)-benzoic acid (HABA)(see mass spectrum on page C-4)MW 242.07 DaApplications:•

Voyager™ Biospectrometry™ Workstation User’s Guide C-11CDithranol(see mass spectrum on page C-5)MW 226.06 DaApplications:Nonpolar synthetic polymersCo

Appendix C MatricesC-12 PerSeptive BiosystemsCtrans-3-indoleacrylic acid (IAA) (see mass spectrum on page C-6)MW 187.2Applications:Non-polar polym

DAppendixVoyager™ Biospectrometry™ Workstation User’s Guide D-1D Log SheetsThis appendix includes log sheets you can copy and use to log samples befo

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-211Voyager-DE PROThe parts of the Voyager-DE PR

AVoyager™ Biospectrometry™ Sample LogPlate #: Date:1234567891012345678910

A.Voyager™ Biospectrometry™ Sample Log Plate: Date: Page of Path and File NameSamp # Matrix Sample Linear Reflector1.2.3.4.5.

A26.27.28.29.30.31.32.33.34.35.36.37.38.39.40.41.42.43.44.45.46.47.48.49.50.Voyager™ Biospectrometry™ Sample Log Plate: Date: Page of

A51.52.53.54.55.56.57.58.59.60.61.62.63.64.65.66.67.68.69.70.71.72.73.74.75.Voyager™ Biospectrometry™ Sample Log Plate: Date: Page of

A76.77.78.79.80.81.82.83.84.85.86.87.88.89.90.91.92.93.94.95.96.97.98.99.100.Voyager™ Biospectrometry™ Sample Log Plate: Date: Page of

AVoyager™ Biospectrometry™ Sample Log Plate: Date: Page of Path and File NameSamp # Matrix Sample Linear Reflector

Appendix D Log SheetsD-8 PerSeptive BiosystemsD

EAppendixVoyager™ Biospectrometry™ Workstation User’s Guide E-1E Grid Voltage%and DelayTime SettingsThe following figures illustrate the relationship

Appendix E Grid Voltage% and Delay Time SettingsE-2 PerSeptive BiosystemsE88 90 92 94 960200400600G rid Voltage (% )Pulse Delay (nsec)m/z=1000m/z=

FAppendixVoyager™ Biospectrometry™ Workstation User’s Guide F-1F ReferenceStandardInformationThis appendix contains the following sections:F.1 Calib

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-22 PerSeptive Biosystems1Parts of the massspectrometerThe Voyager-DE and Voyag

Appendix F Reference Standard InformationF-2 PerSeptive BiosystemsFF.1 Calibration CompoundsThe table below includes masses for common calibratio

Calibration CompoundsVoyager™ Biospectrometry™ Workstation User’s Guide F-3FInsulin B chain, oxidized3493.6435 3495.95 +1 3494.6513 3496.96Adrenocorti

Appendix F Reference Standard InformationF-4 PerSeptive BiosystemsFF.2 Conversion of Mass to Time for Typical StandardsThe table below includes m

Conversion of Mass to Time for Typical StandardsVoyager™ Biospectrometry™ Workstation User’s Guide F-5FBovine Insulin B, Oxidized1 3496.9 3.50E-05 5.5

Appendix F Reference Standard InformationF-6 PerSeptive BiosystemsFF.3 Theoretical Cleavages for AngiotensinMonoisotopic masses (Da) for the theo

Observed PSD Fragments in AngiotensinVoyager™ Biospectrometry™ Workstation User’s Guide F-7FF.4 Observed PSD Fragments in AngiotensinThe masses liste

Appendix F Reference Standard InformationF-8 PerSeptive BiosystemsF272.136 272.3 b2 1000.537 1001.2 a8285.135 285.3 FH 1046.542 1047.2 b8+H2O326.1

GAppendixVoyager™ Biospectrometry™ Workstation User’s Guide G-1G Maintenance LogThe following page includes a log sheet listing maintenance procedur

Maintenance Log for Voyager System Serial Number ____________Record the date and your initials when you perform maintenance procedures.Weekly Jan

HAppendixVoyager™ Biospectrometry™ Workstation User’s Guide H-1H ContinuousExtraction ModeThis appendix contains the following sections:H.1 Optimizi

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-231• Linear detector—A device that detects ions

Appendix H Continuous Extraction ModeH-2 PerSeptive BiosystemsHH.1 Optimizing a Continuous Extraction Standard Instrument (.BIC) SettingBefore yo

Optimizing a Continuous Extraction Standard Instrument (.BIC) SettingVoyager™ Biospectrometry™ Workstation User’s Guide H-3HList of standardinstrument

Appendix H Continuous Extraction ModeH-4 PerSeptive BiosystemsHTable H-2 Continuous Extraction Reflector Mode Standard Instrument Settings (.BIC

Optimizing a Continuous Extraction Standard Instrument (.BIC) SettingVoyager™ Biospectrometry™ Workstation User’s Guide H-5HOptimizationstrategyWhen o

Appendix H Continuous Extraction ModeH-6 PerSeptive BiosystemsH6. Set the Grid Voltage% appropriate for the matrix and mass:7. Save the instrument

Optimizing a Continuous Extraction Standard Instrument (.BIC) SettingVoyager™ Biospectrometry™ Workstation User’s Guide H-7HTable H-5 Guide Wire Vol

Appendix H Continuous Extraction ModeH-8 PerSeptive BiosystemsHH.2 Obtaining Good Spectra in Continuous Extraction ModeThis section describes:• S

Obtaining Good Spectra in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-9HFigure H-1 Example of Poor Mass Spectrum f

Appendix H Continuous Extraction ModeH-10 PerSeptive BiosystemsHFigure H-3 Example of Poor Mass Spectrum for AngiotensinFigure H-4 Example of Go

Obtaining Good Spectra in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-11HParametersaffectingresolution andsignal-to

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-24 PerSeptive Biosystems1The single-stage design provides high mass resolution

Appendix H Continuous Extraction ModeH-12 PerSeptive BiosystemsHH.2.2 Determining Laser Threshold This section describes:•Overview• Adjusting the

Obtaining Good Spectra in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-13HDeterminingthresholdDetermining laser thre

Appendix H Continuous Extraction ModeH-14 PerSeptive BiosystemsHFigure H-5 Saturated Spectrum3. Check the spectrum for the peak of interest. Zoom

Obtaining Good Spectra in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-15HFine-tuningthresholdWhen you determine the

Appendix H Continuous Extraction ModeH-16 PerSeptive BiosystemsHH.2.2.3 Verifying Threshold SettingMove to a new area of the sample well that con

Obtaining Good Spectra in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-17HH.2.3 Checking ResolutionAfter you determ

Appendix H Continuous Extraction ModeH-18 PerSeptive BiosystemsHH.2.4 Fine-Tuning the Laser SettingWhen you find the laser threshold, whether you

Troubleshooting in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-19HH.3 Troubleshooting in ContinuousExtraction Mode

Appendix H Continuous Extraction ModeH-20 PerSeptive BiosystemsHRefer to the table below if you are having spectrum trouble:Signal is flat Laser s

Troubleshooting in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-21HPoor resolution in Continuous Extraction mode(con

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-2511.5.3.1 Voyager-DE Vacuum SystemVacuumchamb

Appendix H Continuous Extraction ModeH-22 PerSeptive BiosystemsHPoor resolution in Continuous Extraction mode(continued)Beam guide wire malfunctio

Troubleshooting in Continuous Extraction ModeVoyager™ Biospectrometry™ Workstation User’s Guide H-23HPoor mass accuracy in Continuous Extraction mode(

Appendix H Continuous Extraction ModeH-24 PerSeptive BiosystemsHPoor mass accuracy in Continuous Extraction mode(continued)Crystals did not form h

IAppendixVoyager™ Biospectrometry™ Workstation User’s Guide I-1I Using the Oscilloscope and Control StickThis appendix contains the following section

Appendix I Using the Oscilloscope and Control StickI-2 PerSeptive BiosystemsIOscilloscopeoverviewAn external oscilloscope (instead of the internal

Guidelines for AcquiringVoyager™ Biospectrometry™ Workstation User’s Guide I-3II.1 Guidelines for AcquiringConsider the following as you acquire a sp

Appendix I Using the Oscilloscope and Control StickI-4 PerSeptive BiosystemsII.2 ScalingInitial scalingInitial scaling of the oscilloscope is det

ScalingVoyager™ Biospectrometry™ Workstation User’s Guide I-5IUse these knobs to adjust the signal on the oscilloscope:• Vertical position—Moves the s

Appendix I Using the Oscilloscope and Control StickI-6 PerSeptive BiosystemsIThe Channel indicator (Ch1 in Figure I-3) displays Ch1 in Linear mode

Using the Control StickVoyager™ Biospectrometry™ Workstation User’s Guide I-7II.3 Using the Control StickStartingacquisitionAfter you load samples on

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-26 PerSeptive Biosystems1Vacuum pumpsTwo vacuum pumps create the vacuum enviro

Appendix I Using the Oscilloscope and Control StickI-8 PerSeptive BiosystemsICAUTIONCheck to see if acquisition has already stopped automatically

Voyager™ Biospectrometry™ Workstation User’s Guide Bibliography-1BBLIIOGRAPHYBibliographyGeneral Mass SpectrometryBeavis, R.C. and B.T. Chait, Chem. P

Bibliography-2 PerSeptive BiosystemsBBLIIOGRAPHYBibliographyKaras, M., U. Bahr, F. Hillenkamp, Int. J. Mass Spectrom. Ion Proc., 1989, 92, 231–242.Nor

BibliographyVoyager™ Biospectrometry™ Workstation User’s Guide Bibliography-3BBLIIOGRAPHYFitzgerald, M.C., L. Zhu, and L.M. Smith, “The Analysis of Mo

Bibliography-4 PerSeptive BiosystemsBBLIIOGRAPHYBibliographyPeptide ApplicationsBieman, K., “Mass Spectrometry of Peptides and Proteins”, Annu. Rev. B

BibliographyVoyager™ Biospectrometry™ Workstation User’s Guide Bibliography-5BBLIIOGRAPHYTang, K., N.I. Taranenko, S.L. Allman, C.H. Chen, L.Y. Chang,

Bibliography-6 PerSeptive BiosystemsBBLIIOGRAPHYBibliography

Voyager™ Biospectrometry™ Workstation User’s Guide Glossary-1GlossaryGOSSLARYa, b, and c ions —Generic description of potential ions that are formed b

Glossary-2 PerSeptive BiosystemsGOSSLARYGlossaryDelay Time —Used in Delayed Extraction mode. Time in nanoseconds (after the laser ionizes the sample)

GlossaryVoyager™ Biospectrometry™ Workstation User’s Guide Glossary-3GOSSLARYIonization —Conversion of sample in solid, gaseous, or liquid phase to io

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-2711.5.3.2 Voyager-DE PRO Vacuum SystemVacuumc

Glossary-4 PerSeptive BiosystemsGOSSLARYGlossaryMatrix —Low-mass, UV-absorbing substance used in MALDI technology to enable sample ionization. Common

GlossaryVoyager™ Biospectrometry™ Workstation User’s Guide Glossary-5GOSSLARYTC2 (Thermocouple vacuum gauge) —Pressure gauge that operates from 1 mill

Glossary-6 PerSeptive BiosystemsGOSSLARYGlossary

Voyager™ Biospectrometry™ Workstation User’s Guide Index-1IndexIDEXNNumerics384 well platePLT file 3-51position/row diagram 3-503-HPAchemical structur

IDEXNIndex-2 PerSeptive BiosystemsIndexAcquiring data, Instrument Control Panel (continued)Automatic Control mode 6-34Data Storage, setting 6-14data,

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-3IDEXNAdobe Acrobat Readerinstalling from Voyager CD 2-26opening PDF Voyager files 2-26A

IDEXNIndex-4 PerSeptive BiosystemsIndexAutomatic Control mode (continued)optimizing BIC for Sequence run 6-65optimizing BIC in Manual Control mode bef

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-5IDEXNBA2, Voyager-DE STRdescription 1-40E09 error 8-25pressure range 1-41pressure, disp

IDEXNIndex-6 PerSeptive BiosystemsIndexCalibration (continued)impact of changing Grid Voltage% 5-41impact of Low Mass Gate 5-79increasing accuracy 3-1

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-7IDEXNCalibration, PSDdefault 7-8default, selecting 7-26equation 7-8in Instrument Settin

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-28 PerSeptive Biosystems1Vacuum pumpsThree vacuum pumps create the vacuum envi

IDEXNIndex-8 PerSeptive BiosystemsIndexComputer (continued)technical support for altered configuration B-1troubleshooting 8-6with Signatec 500 MHz dig

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-9IDEXNCrystallization3-HPA 3-35alpha-cyano 3-34desired pattern 3-34DHB 3-35DHBs 3-35exam

IDEXNIndex-10 PerSeptive BiosystemsIndexDefault calibrationdescription 6-7equation 6-9PSD 7-8selecting 5-10Default layout, Instrument Control Panel 4-

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-11IDEXNDHBschemical structure and molecular weight C-9concentration 3-14crystals 3-14, 3

IDEXNIndex-12 PerSeptive BiosystemsIndexEEjecting sample plates, Instrument Control Panel 4-25Electromagnetic compliance xxiiiEMC standards xxiiiEMIS

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-13IDEXNFore pump, Voyager-DE STRfunction 1-38vacuum gauge 1-40Foreline valve location 1-

IDEXNIndex-14 PerSeptive BiosystemsIndexGuide Wire Voltage%adjusting for CID 7-16description 5-18, 5-46effect of changing 5-46effect on resolution 5-3

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-15IDEXNHot spots in signal intensity 6-5How to use this guide xxviiHPA, see 3-HPAHPLC-gr

IDEXNIndex-16 PerSeptive BiosystemsIndexInstrument Control Panelbasics 4-1BIC loaded at end of Sequence run 6-79control buttons 4-24cursor and grid, d

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-17IDEXNInstrument Settings parameters (continued)Grid Voltage%, Continuous Extraction H-

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-2911.5.4 Vacuum Gauge PanelThe Vacuum Gauge Pa

IDEXNIndex-18 PerSeptive BiosystemsIndexInternal standardcalibration 6-7, 6-25concentration 3-18mass range 3-18Internal-Update calibration, see Calibr

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-19IDEXNLaser (continued)safety information xxvstopping I-7threshold, see Laser threshold

IDEXNIndex-20 PerSeptive BiosystemsIndexLinking traces 4-13Live Spectrum tracedefinition 4-14during acquisition 6-16not displayed on oscilloscope syst

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-21IDEXNManual Laser/Sample Positioning control pagedisplaying 4-27laser position 4-31loc

IDEXNIndex-22 PerSeptive BiosystemsIndexMatrix (continued)selecting 3-3, C-1selecting type in calibration 5-20sinapinic acid 3-3, 3-7, C-6solutions C-

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-23IDEXNNNa adduct ioneffect on masses 8-17from buffer 3-18Nameinstrument, specifying 2-3

IDEXNIndex-24 PerSeptive BiosystemsIndexPPage control, types of 4-9Parent ion, see PSD precursor spectrumPassword, obtaining from system administrator

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-25IDEXNPLT files (continued)search pattern file for 3-57selecting 3-43, 3-45x,y coordina

IDEXNIndex-26 PerSeptive BiosystemsIndexPrinterconnecting, Voyager-DE and Voyager-DE PRO 2-18connecting, Voyager-DE STR 2-20dedicating to landscape or

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-27IDEXNPSD Mirror Ratio (continued)function 7-2precision displayed when you click on ent

Table of Contentsvi PerSeptive BiosystemsChapter 4 Voyager Instrument Control Panel Basics4.1 Instrument Control Panel ...

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-30 PerSeptive Biosystems1• EMIS—Turns BA1 and BA2 on or off. Used during troub

IDEXNIndex-28 PerSeptive BiosystemsIndexPSD segments (continued)mass range 7-34number of, and composite spectrum resolution 7-6number to acquire 7-6,

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-29IDEXNResolution, mass (continued)PSD mode 7-44PSD segment, optimum observed near Max S

IDEXNIndex-30 PerSeptive BiosystemsIndexSample concentration (continued)in IAA 3-15in sinapinic acid 3-7in THAP 3-10low concentration application tech

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-31IDEXNSample plate, types ofapplications for 3-48disposable, applications 3-49disposabl

IDEXNIndex-32 PerSeptive BiosystemsIndexSensitivity (continued)range, Voyager-DE STR 1-6troubleshooting 8-10Vertical Scale parameter, effect on 5-28SE

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-33IDEXNSET file, Sequence Control Panelcreating 6-67defaults used if none specified 6-71

IDEXNIndex-34 PerSeptive BiosystemsIndexSinapinic acidchemical structure and molecular weight C-6concentration 3-7crystals 3-7, 3-34initial velocity s

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-35IDEXNSpectrum window (continued)Grid, displaying 4-21live data, definition 4-14Live Sp

IDEXNIndex-36 PerSeptive BiosystemsIndexTTC2, Voyager-DEdescription 1-26max load pressure 2-32pressure range 1-30wait time 2-32TC2, Voyager-DE PROdesc

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-37IDEXNTraces (continued)types of 4-14white, does not print 4-18zooming 4-13Trihydroxy a

Parts of the Voyager-DE and Voyager-DE PRO SystemsVoyager™ Biospectrometry™ Workstation User’s Guide 1-3111.5.5 Computer ComponentsHardwareThe Voyage

IDEXNIndex-38 PerSeptive BiosystemsIndexVacuum system, Voyager-DE PROsee also Vacuum gauge panelchambers 1-25, 1-27diagram 1-27function 1-24gauges 1-2

IndexVoyager™ Biospectrometry™ Workstation User’s Guide Index-39IDEXNVoyager-DE PRO Biospectrometry Workstation (continued)specifications A-4startup a

IDEXNIndex-40 PerSeptive BiosystemsIndex

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-32 PerSeptive Biosystems11.6 Parts of the Voyager-DE STR SystemThis section d

Parts of the Voyager-DE STR SystemVoyager™ Biospectrometry™ Workstation User’s Guide 1-331Parts of the Voyager-DE STR system include:• Mass spectromet

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-34 PerSeptive Biosystems11.6.2 Mass SpectrometerThe parts of the Voyager-DE S

Parts of the Voyager-DE STR SystemVoyager™ Biospectrometry™ Workstation User’s Guide 1-351Parts of the massspectrometerThe Voyager-DE STR mass spectro

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-36 PerSeptive Biosystems1• Vacuum system—A pumping system and a sealed enclosu

Parts of the Voyager-DE STR SystemVoyager™ Biospectrometry™ Workstation User’s Guide 1-371The single-stage design provides high mass resolution across

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-38 PerSeptive Biosystems11.6.3 Vacuum SystemOverviewThe Voyager-DE STR Biospe

Parts of the Voyager-DE STR SystemVoyager™ Biospectrometry™ Workstation User’s Guide 1-391Figure 1-20 Voyager-DE STR Biospectrometry Workstation Vacu

Table of ContentsVoyager Biospectrometry Workstation User’s Guide vii5.2 Instrument Settings Parameter Descriptions ...

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-40 PerSeptive Biosystems1Vacuum gaugesThe Voyager-DE STR Biospectrometry Works

Parts of the Voyager-DE STR SystemVoyager™ Biospectrometry™ Workstation User’s Guide 1-411CAUTIONDo not press any other buttons on the panel. Pressing

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-42 PerSeptive Biosystems11.6.5 Front Panel IndicatorsThe front panel of the V

Parts of the Voyager-DE STR SystemVoyager™ Biospectrometry™ Workstation User’s Guide 1-4311.6.6 Computer ComponentsHardwareThe Voyager-DE STR Biospec

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-44 PerSeptive Biosystems1SoftwareThe Voyager-DE STR Biospectrometry Workstatio

Software OverviewVoyager™ Biospectrometry™ Workstation User’s Guide 1-4511.7 Software OverviewThe Voyager Biospectrometry Workstation software includ

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-46 PerSeptive Biosystems1• Ability to zoom in on up to four different areas of

Software OverviewVoyager™ Biospectrometry™ Workstation User’s Guide 1-471Sequence ControlPanelThe Sequence Control Panel works in conjunction with the

Chapter 1 Introducing the Voyager™ Biospectrometry™ Workstations1-48 PerSeptive Biosystems11.7.2 Post-Processing Software (Data Explorer)Data E

2ChapterVoyager™ Biospectrometry™ Workstation User’s Guide 2-12 Installing theVoyager™Biospectrometry™WorkstationsThis chapter contains the following

Table of Contentsviii PerSeptive BiosystemsChapter 6 Acquiring Mass Spectra6.1 Before You Begin...

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-2 PerSeptive Biosystems22.1 Installing the SystemYour Voyager Biospectrometry

Selecting the SiteVoyager™ Biospectrometry™ Workstation User’s Guide 2-32Allow 4 inches (10 cm) on the right side of the mass spectrometer for cables.

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-4 PerSeptive Biosystems2To select input voltage:1. Remove the power cord from

Selecting the SiteVoyager™ Biospectrometry™ Workstation User’s Guide 2-52WARNINGFIRE HAZARD. Using a fuse of the wrong type or rating can cause a fire

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-6 PerSeptive Biosystems22.2.2 Voyager-DE STR WorkstationIn this sectionThis s

Connecting Voyager-DE and Voyager-DE PRO WorkstationsVoyager™ Biospectrometry™ Workstation User’s Guide 2-72CAUTIONBefore operation, internal jumpers

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-8 PerSeptive Biosystems22.3.1 Side Panel Diagrams for Mass Spectrometer and C

Connecting Voyager-DE and Voyager-DE PRO WorkstationsVoyager™ Biospectrometry™ Workstation User’s Guide 2-92ComputerDepending on your digitizer option

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-10 PerSeptive Biosystems2Figure 2-4 Digitizer OptionsPB100784CH1 CH2Not usedT

Connecting Voyager-DE and Voyager-DE PRO WorkstationsVoyager™ Biospectrometry™ Workstation User’s Guide 2-1122.3.2 Connecting the Mass Spectrometer t

Table of ContentsVoyager Biospectrometry Workstation User’s Guide ix6.6.6 Process that Occurs when Accumulating Spectra from Multiple Search Pattern

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-12 PerSeptive Biosystems22.3.3 Connecting the Signatec 500 MHz Digitizer Boar

Connecting Voyager-DE and Voyager-DE PRO WorkstationsVoyager™ Biospectrometry™ Workstation User’s Guide 2-1322.3.4 Connecting the LSA1000 LeCroy Digi

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-14 PerSeptive Biosystems2Refer to the following table when connecting the LSA1

Connecting Voyager-DE and Voyager-DE PRO WorkstationsVoyager™ Biospectrometry™ Workstation User’s Guide 2-1522.3.5 Connecting the Tektronix Oscillosc

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-16 PerSeptive Biosystems2Refer to the following table when connecting the osci

Connecting Voyager-DE and Voyager-DE PRO WorkstationsVoyager™ Biospectrometry™ Workstation User’s Guide 2-1722.3.6 Connecting the Video Monitor Figur

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-18 PerSeptive Biosystems2Refer to the following table when connecting the vide

Connecting the Voyager-DE STR WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 2-1922.4 Connecting the Voyager-DE STR WorkstationFigure

Chapter 2 Installing the Voyager™ Biospectrometry™ Workstations2-20 PerSeptive Biosystems2Figure 2-10 Computer Connections for Voyager-DE STR

Connecting the Voyager-DE STR WorkstationVoyager™ Biospectrometry™ Workstation User’s Guide 2-212NOTE: The computer layout may change without notice.