HP Data Explorer 4 Series Manual de usuario

Data Explorer™ SoftwareVersion 4 Series Software User Guide

Table of Contentsx Applied Biosystems

Chapter 3 Peak Detection and Labeling3-2 Applied Biosystems33.1 OverviewThis section includes:• Default peak detection• The resolution-based peak

OverviewData Explorer™ Software User’s Guide 3-333.1.2 The Resolution-BasedPeak Detection RoutineThis section describes:• Type of data affected• Proc

Chapter 3 Peak Detection and Labeling3-4 Applied Biosystems3The software uses the following formula to calculate the expected number of data point

OverviewData Explorer™ Software User’s Guide 3-53Overlapping peakdetection rangesTo accommodate spectral peaks that occur on the boundary of two peak

Chapter 3 Peak Detection and Labeling3-6 Applied Biosystems33.2 Peak DetectionThis section includes:• Strategy for Mariner peak detection• Strate

Peak DetectionData Explorer™ Software User’s Guide 3-733. If peak detection is not acceptable, leave the Use Resolution Dependent Settings option enab

Chapter 3 Peak Detection and Labeling3-8 Applied Biosystems33.2.2 Strategy for Voyager Peak DetectionThis section gives some quick suggestions on

Peak DetectionData Explorer™ Software User’s Guide 3-93• Deisotope (reflector data only)—Peak deisotoping reduces the spectrum to a monoisotopic centr

Chapter 3 Peak Detection and Labeling3-10 Applied Biosystems34. If you see more than one of the problems listed above in a spectrum, you can adjus

Peak DetectionData Explorer™ Software User’s Guide 3-1133.2.3 Setting Peak Detection ParametersThis section includes:• Before you begin• Setting chro

How to Use This GuideData Explorer™ Software User’s Guide xi1How to Use This GuidePurpose ofthis guideThe Applied Biosystems Data Explorer ™ Software

Chapter 3 Peak Detection and Labeling3-12 Applied Biosystems3Figure 3-3 Chromatogram Peak Detection Setup Dialog Box4. Select a detection range a

Peak DetectionData Explorer™ Software User’s Guide 3-133Setting BasicSettings(spectrum data)Basic Settings should provide acceptable peak detection fo

Chapter 3 Peak Detection and Labeling3-14 Applied Biosystems3Figure 3-4 Spectrum Peak Detection Setup—Basic Settings Tab5. If you are detecting P

Peak DetectionData Explorer™ Software User’s Guide 3-153NOTE: Resolution-dependent settings do not apply to Mariner chromatogram data or Voyager PSD d

Chapter 3 Peak Detection and Labeling3-16 Applied Biosystems3Setting PeakProcessingparameters(spectrum dataonly)To set Peak Processing parameters:

Peak DetectionData Explorer™ Software User’s Guide 3-173Setting AdvancedSettings(spectrum dataonly)To set Advanced Settings that you can apply locally

Chapter 3 Peak Detection and Labeling3-18 Applied Biosystems33. Select a detection range, then set parameters as needed.4. Click Apply to accept t

Peak DetectionData Explorer™ Software User’s Guide 3-1933.2.4 Peak Detection Parameter DescriptionsThis section describes:• Chromatogram settings • B

Chapter 3 Peak Detection and Labeling3-20 Applied Biosystems3Detection Ranges(continued)To delete a range, select the range, then click .To combi

Peak DetectionData Explorer™ Software User’s Guide 3-213NOTE: In previous versions of Data Explorer software, peak detection allowed you to specify Pe

How to Use This Guidexii Applied Biosystems1Chapter 5, Examining Spectrum DataDescribes processing and analyzing mass spectral data.Chapter 6, Using T

Chapter 3 Peak Detection and Labeling3-22 Applied Biosystems3Basic Settings(spectrum dataonly)Table 3-2 describes the parameters in the Basic Sett

Peak DetectionData Explorer™ Software User’s Guide 3-233%Max Peak Area Specifies a percentage of the peak with the largest area as the threshold value

Chapter 3 Peak Detection and Labeling3-24 Applied Biosystems3Peak ResolutionMass Resolution Value used to determine the Filter Width used for dete

Peak DetectionData Explorer™ Software User’s Guide 3-253NOTE: In previous versions of Data Explorer software, peak detection allowed you to specify Pe

Chapter 3 Peak Detection and Labeling3-26 Applied Biosystems3Peak Processingparameters(spectrum dataonly)Table 3-3 describes the parameters in the

Peak DetectionData Explorer™ Software User’s Guide 3-273Charge State Determination (Spectrum only)Maximum Charge StateDetermines the peak spacing eval

Chapter 3 Peak Detection and Labeling3-28 Applied Biosystems3AdvancedSettings(spectrum dataonly)Table 3-4 describes the parameters in the Advanced

Peak DetectionData Explorer™ Software User’s Guide 3-293Detection Ranges (continued)You can set multiple, non-contiguous ranges and define parameters

Chapter 3 Peak Detection and Labeling3-30 Applied Biosystems3Active Range ThresholdsNOTE: These settings apply to the Detection Range selected, an

Peak DetectionData Explorer™ Software User’s Guide 3-313Filter SettingsWidth Number of data points used in smoothing for peak detection before integra

How to Use This GuideData Explorer™ Software User’s Guide xiii1Conventions This guide uses the following conventions to make text easier to understand

Chapter 3 Peak Detection and Labeling3-32 Applied Biosystems33.2.5 Charge StateDetermination and ExamplesNOTE: Isotope-resolved peaks in Voyager

Peak DetectionData Explorer™ Software User’s Guide 3-333Max Charge Stateand Max Isotope #set correctlyWhen the Max Charge State and Max Isotope # are

Chapter 3 Peak Detection and Labeling3-34 Applied Biosystems3.Figure 3-8 Max Charge State Set Too Low and Max Isotope # Set CorrectlyThe grouping

Peak DetectionData Explorer™ Software User’s Guide 3-353Max Isotope #set too lowIf the Max Isotope # is set too low, the software incorrectly groups p

Chapter 3 Peak Detection and Labeling3-36 Applied Biosystems3Effect of MinimumIntensityThe Minimum Intensity setting on the Advanced Settings tab

Peak ListData Explorer™ Software User’s Guide 3-3733.3 Peak ListThis section describes:• Displaying the peak list• Inserting peaks in the peak list•

Chapter 3 Peak Detection and Labeling3-38 Applied Biosystems3Contentsof peak listThe peak lists contain the following information.Chromatogrampeak

Peak ListData Explorer™ Software User’s Guide 3-3933.3.2 Inserting Peaks in the Peak ListDescription If chromatogram or spectrum peaks are not detect

Chapter 3 Peak Detection and Labeling3-40 Applied Biosystems3Inserted peaks are:• Removed from the list when you close the data file, reprocess th

Peak ListData Explorer™ Software User’s Guide 3-413NOTE: Inserted peaks are included when you save a .PKT file.NOTE: Peak list headings are not includ

How to Use This Guidexiv Applied Biosystems1RelateddocumentationThe related documents shipped with your system include:• Mariner ™ Workstation User’s

Chapter 3 Peak Detection and Labeling3-42 Applied Biosystems33.3.4 Sorting, Filtering, and Printing the Peak ListSortingthe peak listThe peak lis

Peak ListData Explorer™ Software User’s Guide 3-4332. Select Enable Peak List Filter, then select:Filter Type DescriptionMonoisotopic Labels the peak

Chapter 3 Peak Detection and Labeling3-44 Applied Biosystems3Printingthe peak listTo print the peak list:1. Display the peak list as you want it p

Deisotoping a SpectrumData Explorer™ Software User’s Guide 3-4533.4 Deisotoping a SpectrumThis section includes:• Description• During peak deisotopin

Chapter 3 Peak Detection and Labeling3-46 Applied Biosystems3If the expected higher theoretical peak masses and areas are present in the peak list

Deisotoping a SpectrumData Explorer™ Software User’s Guide 3-473Figure 3-17 Interpreting a Deisotoped TraceRequirements The Deisotope function requir

Chapter 3 Peak Detection and Labeling3-48 Applied Biosystems3Using theDeisotopefunctionTo use the Deisotope function:1. Display the spectrum trace

Deisotoping a SpectrumData Explorer™ Software User’s Guide 3-493CAUTIONIf you enter an invalid value in the Adduct field, for example, numbers, the sp

Chapter 3 Peak Detection and Labeling3-50 Applied Biosystems3Example Figure 3-19 and Figure 3-20 illustrate the effects of deisotoping.Before deis

Deisotoping a SpectrumData Explorer™ Software User’s Guide 3-513Returning to theoriginal spectrumTo return to the original spectrum:• If the original

1ChapterData Explorer™ Software User’s Guide 1-11 Data Explorer™ BasicsThis chapter contains the following sections:1.1 Overview ...

Chapter 3 Peak Detection and Labeling3-52 Applied Biosystems33.5 Peak LabelingThis section includes:• Charge state labels• Setting chromatogram a

Peak LabelingData Explorer™ Software User’s Guide 3-5333.5.1 Charge State LabelsCharge statelabelsA unique feature of the Data Explorer software is t

Chapter 3 Peak Detection and Labeling3-54 Applied Biosystems3• Isotopes must be resolved• Peak detection parameters must be set to detect all of t

Peak LabelingData Explorer™ Software User’s Guide 3-553Figure 3-21 Chromatogram Peak Label Dialog Box3. Select Enable Labeling. 4. Set the number of

Chapter 3 Peak Detection and Labeling3-56 Applied Biosystems38. Click OK. The trace is displayed. The detected peaks that meet the peak labeling c

Peak LabelingData Explorer™ Software User’s Guide 3-5735. Select the Mass Type (peak apex or peak centroid).6. Select the Peak Mass Label Type:Label D

Chapter 3 Peak Detection and Labeling3-58 Applied Biosystems37. Select label attributes:• Overlapping—Allows labels to be displayed when peaks are

Peak LabelingData Explorer™ Software User’s Guide 3-593If peak list filtering is enabled, only the detected peaks that meet the peak filtering criteri

Chapter 3 Peak Detection and Labeling3-60 Applied Biosystems3Charge statenot displayedIf no charge is displayed, there are a few possible causes:•

Peak LabelingData Explorer™ Software User’s Guide 3-6133.5.3 Setting Custom Peak LabelsThis section includes:• Description• Customizing colors, font,

Chapter 1 Data Explorer™ Basics1-2 Applied Biosystems11.1 OverviewDescription The Data Explorer™ Version 4.0 processing software is graphical sof

Chapter 3 Peak Detection and Labeling3-62 Applied Biosystems3Figure 3-23 User Label Setup Dialog Box 4. Select the Label Type (spectra only):• Ma

Peak LabelingData Explorer™ Software User’s Guide 3-6336. To manually enter label settings, click . The User Label Entry dialog box is displayed (Fig

Chapter 3 Peak Detection and Labeling3-64 Applied Biosystems3To enter Peak Mass, X Value, or Mass Difference, you can type values or right-click-d

Peak LabelingData Explorer™ Software User’s Guide 3-653Applying userlabels from .LBCor .LBS filesYou can apply labels you previously created and saved

Chapter 3 Peak Detection and Labeling3-66 Applied Biosystems3User labels notdisplayedIf a user label is not displayed or is displayed incorrectly,

Process that Occurs During Peak Detection, Centroiding, and IntegrationData Explorer™ Software User’s Guide 3-6733.6 Process that Occurs During Peak

Chapter 3 Peak Detection and Labeling3-68 Applied Biosystems3• For spectral data, determines the peak boundaries by one of two means:• If the Nois

Process that Occurs During Peak Detection, Centroiding, and IntegrationData Explorer™ Software User’s Guide 3-693After peakdetectionAfter peaks are de

Chapter 3 Peak Detection and Labeling3-70 Applied Biosystems3Integration The Data Explorer software integrates chromatographic and spectral peaks

Default Peak Detection SettingsData Explorer™ Software User’s Guide 3-7133.7 Default Peak Detection SettingsThis section includes:• Default .SET file

OverviewData Explorer™ Software User’s Guide 1-31Starting andexiting thesoftwareTo start the Data Explorer software from the Windows NT desktop, doubl

Chapter 3 Peak Detection and Labeling3-72 Applied Biosystems3The following table lists the default settings in the .SET files provided for spectra

Default Peak Detection SettingsData Explorer™ Software User’s Guide 3-733AdditionalVoyager .SET filesprovidedAdditional .SET files that have been deve

Chapter 3 Peak Detection and Labeling3-74 Applied Biosystems3

4ChapterData Explorer™ Software User’s Guide 4-14 Examining Chromatogram Data This chapter contains the following sections:4.1 Overview ...

Chapter 4 Examining Chromatogram Data4-2 Applied Biosystems44.1 OverviewThis section includes:• Types of Mariner data• Types of Voyager data• Cre

OverviewData Explorer™ Software User’s Guide 4-34You can display extracted chromatograms from Mariner data files by selecting the Process menu with a

Chapter 4 Examining Chromatogram Data4-4 Applied Biosystems4You can display the following types of Voyager data by selecting Extracted Ion from th

Creating an Extracted Ion ChromatogramData Explorer™ Software User’s Guide 4-544.2 Creating an Extracted Ion ChromatogramThis section includes:• Crea

Chapter 4 Examining Chromatogram Data4-6 Applied Biosystems44. In the Extracted Ion Chromatogram dialog box (Figure 4-1 on page 4-7), select one o

Creating an Extracted Ion ChromatogramData Explorer™ Software User’s Guide 4-74Figure 4-1 Extracted Ion Chromatogram Dialog Box5. Specify the Extract

Chapter 1 Data Explorer™ Basics1-4 Applied Biosystems1Figure 1-2 Data Explorer Window with Voyager DataDefault colors The default colors are diff

Chapter 4 Examining Chromatogram Data4-8 Applied Biosystems4From theSpectrum windowTo create an extracted ion chromatogram for a mass range from t

Creating an Extracted Ion ChromatogramData Explorer™ Software User’s Guide 4-944.2.2 Creating a Constant Neutral Loss (CNL) Chromatogram This section

Chapter 4 Examining Chromatogram Data4-10 Applied Biosystems4Labelingspectrum peakswith massdifference(optional)You can label spectrum peaks with

Creating an Extracted Ion ChromatogramData Explorer™ Software User’s Guide 4-1145. Type in the Mass Difference and Tolerance.NOTE: Do not right-click-

Chapter 4 Examining Chromatogram Data4-12 Applied Biosystems4Example Figure 4-4 shows a TIC that contains three flavonoid compound peaks. To deter

Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)Data Explorer™ Software User’s Guide 4-1344.3 Creating an Extracted Absorbance

Chapter 4 Examining Chromatogram Data4-14 Applied Biosystems4Figure 4-6 Extracted Absorbance Chromatogram Dialog Box6. Specify the Extraction Mod

Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)Data Explorer™ Software User’s Guide 4-154From theSpectrum windowTo create an e

Chapter 4 Examining Chromatogram Data4-16 Applied Biosystems4Figure 4-7 Extracted Absorbance Chromatogram7. To return to the original trace, see

Noise Filtering/SmoothingData Explorer™ Software User’s Guide 4-1744.4 Noise Filtering/SmoothingDescription The Noise Filter/Smooth command provides

File Formats and TypesData Explorer™ Software User’s Guide 1-511.2 File Formats and TypesThis section describes:• Software applications compatibility

Chapter 4 Examining Chromatogram Data4-18 Applied Biosystems42. Select the method to use based upon the type of data you are examining, then enter

Noise Filtering/SmoothingData Explorer™ Software User’s Guide 4-1943. Click OK.The trace is displayed with an NF, SM, or NR trace label.4. To return t

Chapter 4 Examining Chromatogram Data4-20 Applied Biosystems44.5 Adding and SubtractingRaw Spectra Within a Data FileUse the Add/Subtract Spectra

Adding and Subtracting Raw Spectra Within a Data FileData Explorer™ Software User’s Guide 4-214Figure 4-9 .Add and Subtract Spectra Dialog Box4. Sel

Chapter 4 Examining Chromatogram Data4-22 Applied Biosystems4NOTE: Before you can subtract spectra, you must first specify spectra to be added.6.

Displaying MS Method Data (Mariner Data Only)Data Explorer™ Software User’s Guide 4-2344.6 Displaying MS Method Data(Mariner Data Only)Overview If yo

Chapter 4 Examining Chromatogram Data4-24 Applied Biosystems4Hint: Add mode is useful when you filter the same trace for different event tags. The

Displaying MS Method Data (Mariner Data Only)Data Explorer™ Software User’s Guide 4-254NOTE: Only tags present in the data file are available.6. Selec

Chapter 4 Examining Chromatogram Data4-26 Applied Biosystems4Hint: Add mode is useful when you are filtering the same trace for different event ta

Adjusting the BaselineData Explorer™ Software User’s Guide 4-2744.7 Adjusting the BaselineThis section includes:• Using Baseline Offset• Using Baseli

© Copyright 2001, Applied Biosystems. All rights reserved.For Research Use Only. Not for use in diagnostic procedures.Information in this document is

Chapter 1 Data Explorer™ Basics1-6 Applied Biosystems1Mariner .SPC fileformatIn Mariner software versions earlier than version 3.0, data files are

Chapter 4 Examining Chromatogram Data4-28 Applied Biosystems4Figure 4-12 Baseline Offset Dialog Box4. Right-click-drag the left baseline to offse

Adjusting the BaselineData Explorer™ Software User’s Guide 4-2944.7.2 Using Baseline CorrectionDescription The Baseline Correction feature is a funct

Chapter 4 Examining Chromatogram Data4-30 Applied Biosystems44.8 Using UV Trace Offset(Mariner Data Only)To align a UV trace with a chromatogram

Using UV Trace Offset (Mariner Data Only)Data Explorer™ Software User’s Guide 4-3146. Click OK.The UV trace peak is shifted to align with the chromato

Chapter 4 Examining Chromatogram Data4-32 Applied Biosystems4

5ChapterData Explorer™ Software User’s Guide 5-15 Examining Spectrum DataThis chapter contains the following sections:5.1 Overview ...

Chapter 5 Examining Spectrum Data5-2 Applied Biosystems55.1 OverviewTypes of spectrayou can displayYou can display the following types of spectru

OverviewData Explorer™ Software User’s Guide 5-35Returning to theoriginal spectrumMany processing functions generate a new trace. If you have Trace Re

Chapter 5 Examining Spectrum Data5-4 Applied Biosystems55.2 Creating a Combined Spectrum NOTE: Before creating a combined spectrum for Voyager mu

Manual CalibrationData Explorer™ Software User’s Guide 5-555.3 Manual CalibrationThis section describes:• Overview of manual calibration• Manually ca

File Formats and TypesData Explorer™ Software User’s Guide 1-71Settings(continued).MSM (Mariner only)MS Method settings, if data was acquired using an

Chapter 5 Examining Spectrum Data5-6 Applied Biosystems5The manual calibration feature provides two modes for peak matching:• Automatic—The softwa

Manual CalibrationData Explorer™ Software User’s Guide 5-755.3.2 Manually CalibratingThis section describes:• Before calibrating Voyager data• Manual

Chapter 5 Examining Spectrum Data5-8 Applied Biosystems5Manuallycalibrating asingle spectrumNOTE: Multi-point calibration yields higher mass accur

Manual CalibrationData Explorer™ Software User’s Guide 5-95Figure 5-2 Manual Mass Calibration Dialog Box 4. Select a calibration reference file. For

Chapter 5 Examining Spectrum Data5-10 Applied Biosystems56. Select the Peak Weighting Factor. If the calibration includes more than two points, yo

Manual CalibrationData Explorer™ Software User’s Guide 5-1158. Do any of the following:• Click OK to accept the selected reference mass for matching,

Chapter 5 Examining Spectrum Data5-12 Applied Biosystems59. Repeat step 7 and step 8 until all desired peaks are in the matched list.Eliminating d

Manual CalibrationData Explorer™ Software User’s Guide 5-135Figure 5-4 Eliminate Fit Outlier Deletes the Match with the Largest Fit Error from the Ou

Chapter 5 Examining Spectrum Data5-14 Applied Biosystems5Figure 5-5 Calibration Statistics in Output Window If you calibrate more than once, subs

Manual CalibrationData Explorer™ Software User’s Guide 5-155NOTE: If you are calibrating Mariner data, see “Ensuring that masses match during calibrat

Chapter 1 Data Explorer™ Basics1-8 Applied Biosystems1Additional filestypesAdditional file types you may see on your system are described below.Ta

Chapter 5 Examining Spectrum Data5-16 Applied Biosystems5Exportingcalibrationconstants(.CAL file)The calculated calibration constants can be expor

Manual CalibrationData Explorer™ Software User’s Guide 5-1755. To save the calibration to the data file, select Mass Calibration from the Process menu

Chapter 5 Examining Spectrum Data5-18 Applied Biosystems5Definition A calibration reference file (.REF) is a list of masses and corresponding info

Manual CalibrationData Explorer™ Software User’s Guide 5-195The Edit/Create Reference Peak Information dialog box (Figure 5-6) is displayed.Figure 5-6

Chapter 5 Examining Spectrum Data5-20 Applied Biosystems5CAUTIONThe software allows you to add multiple items with the same m/z value to the refer

Manual CalibrationData Explorer™ Software User’s Guide 5-2153. To modify an entry, click the entry to select it, modify the entry as needed, then clic

Chapter 5 Examining Spectrum Data5-22 Applied Biosystems55.3.4 Reverting to Instrument CalibrationThe Revert to Instrument Calibration function d

Manual CalibrationData Explorer™ Software User’s Guide 5-235If you apply the calibration, the next time you open the data file, the MC trace label is

Chapter 5 Examining Spectrum Data5-24 Applied Biosystems55.3.5 Hints for Calibrating Mariner DataEnsuring thatmasses matchduring calibrationMarin

Manual CalibrationData Explorer™ Software User’s Guide 5-2555.3.6 Hints for Calibrating Voyager DataImporting acalibrationIf you import a calibration

File Formats and TypesData Explorer™ Software User’s Guide 1-91Reference .REF List of masses to select from during calibration. See “Creating and savi

Chapter 5 Examining Spectrum Data5-26 Applied Biosystems55.4 Automatic CalibrationThis section includes:• Overview of automatic calibration• Impo

Automatic CalibrationData Explorer™ Software User’s Guide 5-275• Matches all peaks that meet the specified Reference Matching criteria. If the number

Chapter 5 Examining Spectrum Data5-28 Applied Biosystems5When to use Use automatic calibration for Mariner data when you:• Have many spectra to ca

Automatic CalibrationData Explorer™ Software User’s Guide 5-2955.4.2 Importing and Specifying Automatic Calibration Settings ImportingHint: Importing

Chapter 5 Examining Spectrum Data5-30 Applied Biosystems52. From the Peaks menu, select Peak Label, then set the Mass Label Type to Centroid. NOTE

Automatic CalibrationData Explorer™ Software User’s Guide 5-3155. To add up to 10 reference masses to the Masses to Match list, do either of the follo

Chapter 5 Examining Spectrum Data5-32 Applied Biosystems56. Specify reference masses to add by doing either of the following:• Click a mass, then

Automatic CalibrationData Explorer™ Software User’s Guide 5-33510. Select the Peak Weighting Factor. If the calibration includes more than two points,

Chapter 5 Examining Spectrum Data5-34 Applied Biosystems55.4.3 Automatically Calibrating (Mariner Data Only) This section includes:• Automaticall

Automatic CalibrationData Explorer™ Software User’s Guide 5-355Applying newconstants to thedata fileTo save the calibration constants for each spectru

Chapter 1 Data Explorer™ Basics1-10 Applied Biosystems1Process(continued).RCD Chromatogram results file exported from .DAT files. See Section 2.7,

Chapter 5 Examining Spectrum Data5-36 Applied Biosystems55.5 CentroidingNOTE: Centroiding is not supported for Mariner DAD data.To display peaks

Mass Deconvolution (Mariner Data Only)Data Explorer™ Software User’s Guide 5-3755.6 Mass Deconvolution (Mariner Data Only)NOTE: Mass deconvolution is

Chapter 5 Examining Spectrum Data5-38 Applied Biosystems5The Multiply Charged Deconvolution dialog box (Figure 5-11) is displayed.4. In the Spectr

Mass Deconvolution (Mariner Data Only)Data Explorer™ Software User’s Guide 5-3956. Select the method to use for calculation:• Automatic—Selects additi

Chapter 5 Examining Spectrum Data5-40 Applied Biosystems511. Click OK. The result is displayed in the Output window and the zero-charge spectrum i

Mass Deconvolution (Mariner Data Only)Data Explorer™ Software User’s Guide 5-4155. Type values for the following masses for the generated zero-charge

Chapter 5 Examining Spectrum Data5-42 Applied Biosystems55.7 Noise Filtering/SmoothingDescription The Noise Filter/Smooth function includes four

Noise Filtering/SmoothingData Explorer™ Software User’s Guide 5-4353. Select the method to use based on the type of data you are examining, then enter

Chapter 5 Examining Spectrum Data5-44 Applied Biosystems54. Click OK.The trace is displayed with an RSM, NF, NR or SM trace label.5. To return to

Adjusting the BaselineData Explorer™ Software User’s Guide 5-4555.8 Adjusting the BaselineThis section includes:• Using Baseline Offset• Using Baseli

Parts of the Data Explorer WindowData Explorer™ Software User’s Guide 1-1111.3 Parts of the Data Explorer WindowThis section describes:• Overview• To

Chapter 5 Examining Spectrum Data5-46 Applied Biosystems5Figure 5-14 Baseline Offset Dialog Box4. Right-click-drag the left baseline to offset. T

Adjusting the BaselineData Explorer™ Software User’s Guide 5-4755.8.2 Using Baseline CorrectionDescription The Baseline Correction function corrects

Chapter 5 Examining Spectrum Data5-48 Applied Biosystems55.8.3 Using Advanced Baseline Correction This section includes:• Description• When to us

Adjusting the BaselineData Explorer™ Software User’s Guide 5-495When to use Use advanced baseline correction if you are analyzing data with an offset

Chapter 5 Examining Spectrum Data5-50 Applied Biosystems53. Enter parameters as described below. These parameters interact with each other and req

Adjusting the BaselineData Explorer™ Software User’s Guide 5-515Peak Width (at half height)(continued)Set Peak Width according to the data you are cor

Chapter 5 Examining Spectrum Data5-52 Applied Biosystems5Flexibility With the Peak Width parameter, determines the number of points used to estima

Adjusting the BaselineData Explorer™ Software User’s Guide 5-535NOTE: Flexibility and Degree parameters may require some testing to determine the opti

Chapter 5 Examining Spectrum Data5-54 Applied Biosystems5Generalguidelines forsettingparametersRefer to the following table to determine how to se

Adjusting the BaselineData Explorer™ Software User’s Guide 5-555Troubleshooting If the baseline rises preceding and following a peak after the correct

Chapter 1 Data Explorer™ Basics1-12 Applied Biosystems1Toolbar The toolbar contains buttons that access Data Explorer functions.For a description

Chapter 5 Examining Spectrum Data5-56 Applied Biosystems55.9 Truncating a SpectrumDescription The Truncate function removes data points from a tr

Truncating a SpectrumData Explorer™ Software User’s Guide 5-575The data in the spectrum is truncated to the selected range and is displayed with a TR

Chapter 5 Examining Spectrum Data5-58 Applied Biosystems5Figure 5-19 Truncated Spectrum—Low Mass Gate Spike Eliminated

Converting to a Singly Charged Spectrum (Mariner Data Only)Data Explorer™ Software User’s Guide 5-5955.10 Converting to a Singly Charged Spectrum (Ma

Chapter 5 Examining Spectrum Data5-60 Applied Biosystems53. Select Duplicate Active Trace from the Display menu to keep the original data displaye

Converting to a Singly Charged Spectrum (Mariner Data Only)Data Explorer™ Software User’s Guide 5-615Example Figure 5-21 and Figure 5-22 illustrate th

Chapter 5 Examining Spectrum Data5-62 Applied Biosystems5NOTE: Charge states other than 0 or 1 in the converted trace indicate that a peak in the

AutoSaturation Correction (Mariner Data Only)Data Explorer™ Software User’s Guide 5-635Effect on Mariner.RST filesThe AutoSaturation Correction featur

Chapter 5 Examining Spectrum Data5-64 Applied Biosystems55.12 Adding and Subtracting Raw or Processed Spectra from the Same or Different Data Fil

Adding and Subtracting Raw or Processed Spectra from the Same or Different Data Files (DualData Explorer™ Software User’s Guide 5-655Figure 5-23 Dual

Parts of the Data Explorer WindowData Explorer™ Software User’s Guide 1-131SPEC Displays the spectrum for the selected time in the TIC or TAC trace. B

Chapter 5 Examining Spectrum Data5-66 Applied Biosystems5

6ChapterData Explorer™ Software User’s Guide 6-16 Using Tools and ApplicationsThis chapter contains the following sections:6.1 Using the Elemental C

Chapter 6 Using Tools and Applications6-2 Applied Biosystems66.1 Using the Elemental Composition CalculatorThis section includes:• Determining el

Using the Elemental Composition CalculatorData Explorer™ Software User’s Guide 6-36Procedure To determine elemental composition:1. Display the spectru

Chapter 6 Using Tools and Applications6-4 Applied Biosystems64. Enter m/z values in the m/z ratio list by doing any of the following:• Right-click

Using the Elemental Composition CalculatorData Explorer™ Software User’s Guide 6-56•“Adding new elements and setting limits” on page 6-9•“Setting limi

Chapter 6 Using Tools and Applications6-6 Applied Biosystems6Hint: You can sort the results in a column by clicking the column header.Results incl

Using the Elemental Composition CalculatorData Explorer™ Software User’s Guide 6-76Displaying thetheoreticalisotopedistributionTo display the theoreti

Chapter 6 Using Tools and Applications6-8 Applied Biosystems62. To change the limits for an element, double-click an element to display the Isotop

Using the Elemental Composition CalculatorData Explorer™ Software User’s Guide 6-96Adding newelements andsetting limitsTo add new elements and set lim

Chapter 1 Data Explorer™ Basics1-14 Applied Biosystems1Labels in the chromatogram or spectrum title identify the type of data displayed in the win

Chapter 6 Using Tools and Applications6-10 Applied Biosystems6Figure 6-6 Periodic Table3. Click an element to select it and to display the Isotop

Using the Elemental Composition CalculatorData Explorer™ Software User’s Guide 6-116Figure 6-7 Isotope Dialog BoxNOTE: Ignore the column of check box

Chapter 6 Using Tools and Applications6-12 Applied Biosystems6Setting limits forother result typesTo set limits for amino acid, DNA, RNA, or carbo

Using the Isotope CalculatorData Explorer™ Software User’s Guide 6-1366.2 Using the Isotope CalculatorDescription Use the Isotope calculator to gener

Chapter 6 Using Tools and Applications6-14 Applied Biosystems64. Select the Formula or Sequence for the type of isotope to calculate.5. Select a f

Using the Isotope CalculatorData Explorer™ Software User’s Guide 6-1567. Specify the Add/Subtract Group option. To enable or disable the option, selec

Chapter 6 Using Tools and Applications6-16 Applied Biosystems610. Select the calculation mode: • FWHM—Resolves peaks using the full peak width at

Using the Isotope CalculatorData Explorer™ Software User’s Guide 6-176To calculate a theoretical isotope distribution for doubly sodiated and deproton

Chapter 6 Using Tools and Applications6-18 Applied Biosystems6Evaluating traces The theoretical isotope distribution is displayed in the Spectrum

Using the Isotope CalculatorData Explorer™ Software User’s Guide 6-196Results The results of the calculation are displayed in the Result tab of Output

Parts of the Data Explorer WindowData Explorer™ Software User’s Guide 1-151Output window The Output window (see Figure 1-3 on page 1-11) displays tabs

Chapter 6 Using Tools and Applications6-20 Applied Biosystems66.3 Using the Mass Resolution CalculatorCalculating massresolutionTo calculate mass

Using the Mass Resolution CalculatorData Explorer™ Software User’s Guide 6-216Figure 6-12 Mass Resolution Calculator5. Specify the peak for which to

Chapter 6 Using Tools and Applications6-22 Applied Biosystems6The result is displayed in the Output window (Figure 6-13).Figure 6-13 Resolution C

Using the Signal-to-Noise Ratio CalculatorData Explorer™ Software User’s Guide 6-2366.4 Using the Signal-to-Noise Ratio CalculatorDescription A signa

Chapter 6 Using Tools and Applications6-24 Applied Biosystems63. Select the method to use, then right-click-drag on peaks in the trace to enter th

Using the Ion Fragmentation CalculatorData Explorer™ Software User’s Guide 6-2566.5 Using the Ion Fragmentation Calculator Description The Ion Fragme

Chapter 6 Using Tools and Applications6-26 Applied Biosystems6Figure 6-15 Ion Fragmentation Calculator Dialog Box 4. Type or copy the amino acid

Using the Ion Fragmentation CalculatorData Explorer™ Software User’s Guide 6-276Setting Options 7. Click Options.The Ion Fragmentation Options dialog

Chapter 6 Using Tools and Applications6-28 Applied Biosystems6Settinguser-defined aminoacids13. Click User-Defined Amino Acids.The User-Defined Am

Using the Ion Fragmentation CalculatorData Explorer™ Software User’s Guide 6-296Figure 6-18 Ion Fragmentation Results for Synthetic Peptide (PPPPPPPP

Table of Contents Data Explorer™ Software User’s Guide iiiTable of Contents How to Use This Guide...

Chapter 1 Data Explorer™ Basics1-16 Applied Biosystems1• Instrument Setting—Displays a list of instrument settings used to obtain the data. The se

Chapter 6 Using Tools and Applications6-30 Applied Biosystems6Labeling peaks Click Label Peaks. The ion peaks specified in the Options dialog box

Using the Elemental Targeting ApplicationData Explorer™ Software User’s Guide 6-3166.6 Using the Elemental Targeting ApplicationDescription The Eleme

Chapter 6 Using Tools and Applications6-32 Applied Biosystems6Note the following when entering formulas:• Spaces do not matter for formula. The fi

Using the Elemental Targeting ApplicationData Explorer™ Software User’s Guide 6-336Displaying results The results of the calculation are displayed in

Chapter 6 Using Tools and Applications6-34 Applied Biosystems66.7 Using the Macro RecorderDescription The Macro Recorder feature in Data Explorer

Using the Macro RecorderData Explorer™ Software User’s Guide 6-356Location ofmacrosAll macros you record are stored in a file called DATAEXPLORER.VB6

Chapter 6 Using Tools and Applications6-36 Applied Biosystems6Functions you perform in the Output window, for example, sorting or copying the peak

Using the Macro RecorderData Explorer™ Software User’s Guide 6-3766.7.2 Recording a MacroTo record a macro:1. Open a data file.2. From the Tools menu

Chapter 6 Using Tools and Applications6-38 Applied Biosystems66.7.3 Assigning Macros to ButtonsOnly macros present in the DATAEXPLORER.VB6 file c

Using the Macro RecorderData Explorer™ Software User’s Guide 6-396De-assigning amacro from abuttonTo de-assign a macro from a button, select the macro

Customizing the Data Explorer WindowData Explorer™ Software User’s Guide 1-1711.4 Customizing theData Explorer WindowThis section includes:• Setting

Chapter 6 Using Tools and Applications6-40 Applied Biosystems6Figure 6-25 Macros Dialog Box 3. Select the macro to run from the list.4. Click Run

Using the Macro RecorderData Explorer™ Software User’s Guide 6-4166.7.5 Deleting a MacroTo delete a macro:1. From the Tools menu, select Macros.The

Chapter 6 Using Tools and Applications6-42 Applied Biosystems66.7.6 Advanced Macro EditingAccessing theVisual BasicEditorYou can access the Visua

Using the Macro RecorderData Explorer™ Software User’s Guide 6-4366.7.7 Importing or Exporting Macros in DATAEXPLORER.VB6You can import macros into,

Chapter 6 Using Tools and Applications6-44 Applied Biosystems6The selected macros are imported into the DATAEXPLORER.VB6 project. The .BAS files a

Using the Macro RecorderData Explorer™ Software User’s Guide 6-4566.7.8 Running Macros Automatically When Opening and Closing FilesYou can set the Da

Chapter 6 Using Tools and Applications6-46 Applied Biosystems6

7ChapterData Explorer™ Software User’s Guide 7-17 Data Explorer ExamplesThis chapter contains the following sections:7.1 Mariner Data Examples ...

Chapter 7 Data Explorer Examples7-2 Applied Biosystems77.1 Mariner Data ExamplesThis section includes:• Improving signal-to-noise ratio• Deconvol

Mariner Data ExamplesData Explorer™ Software User’s Guide 7-37Figure 7-1 illustrates the improved signal-to-noise ratio in the extracted ion chromatog

Chapter 1 Data Explorer™ Basics1-18 Applied Biosystems1Overview ofprocessing andgraphic settingsProcessing and graphic settings control how data i

Chapter 7 Data Explorer Examples7-4 Applied Biosystems77.1.2 Deconvoluting and Evaluating Unresolved Chromatographic PeaksOverview You can use th

Mariner Data ExamplesData Explorer™ Software User’s Guide 7-57The combined spectrum is displayed (Figure 7-3), with two intense peaks at 410 Da and 72

Chapter 7 Data Explorer Examples7-6 Applied Biosystems7Figure 7-4 Deconvoluting Unresolved Chromatographic PeaksCreatingcombined spectraCreate a

Mariner Data ExamplesData Explorer™ Software User’s Guide 7-77Figure 7-5 illustrates the combined spectra for the deconvoluted peaks.Note that both sp

Chapter 7 Data Explorer Examples7-8 Applied Biosystems77.1.3 Determining if a Peak is Background NoiseOverview To determine if spectral peaks rep

Mariner Data ExamplesData Explorer™ Software User’s Guide 7-97The spectrum range is displayed in the Spectra To Be Subtracted list in the Add and Subt

Chapter 7 Data Explorer Examples7-10 Applied Biosystems7Figure 7-7 Subtracted SpectrumThe peak at 391 is still present, which indicates one of th

Voyager Data ExamplesData Explorer™ Software User’s Guide 7-1177.2 Voyager Data ExamplesThis section includes:• Detecting and labeling partially reso

Chapter 7 Data Explorer Examples7-12 Applied Biosystems7Figure 7-9 Partially Resolved Peaks That Represent Two Compounds, Minor Component Not Det

Voyager Data ExamplesData Explorer™ Software User’s Guide 7-1372. Do either of the following:• Change the %Max Peak Area from 1 (the default) to 0, an

Customizing the Data Explorer WindowData Explorer™ Software User’s Guide 1-191Additional .SET files that have been developed for detection of differen

Chapter 7 Data Explorer Examples7-14 Applied Biosystems77.2.2 Processing Before Calibrating to Optimize Mass AccuracyThis section includes:• Cali

Voyager Data ExamplesData Explorer™ Software User’s Guide 7-157Before calibrating To optimize mass accuracy, do the following before calibrating:1. Di

Chapter 7 Data Explorer Examples7-16 Applied Biosystems7Calibrating To calibrate the deisotoped spectrum:1. From the Peaks menu, select Peak Label

Voyager Data ExamplesData Explorer™ Software User’s Guide 7-177Matching peaks 5. Click Match Peaks and Solve. The software compares observed masses in

Chapter 7 Data Explorer Examples7-18 Applied Biosystems77.2.3 Detecting Peaks from Complex DigestsOverview Complex digests often contain hundreds

Voyager Data ExamplesData Explorer™ Software User’s Guide 7-197Procedure To detect peaks from complex mixtures:1. Display the spectrum of interest.Noi

Chapter 7 Data Explorer Examples7-20 Applied Biosystems7Figure 7-20 Spectrum Peak Detection Setup—Basic Settings Tab5. Click Use Advanced Setting

Voyager Data ExamplesData Explorer™ Software User’s Guide 7-217Figure 7-21 Spectrum Peak Detection Setup—Advanced Settings Tab 6. Set Minimum Area to

Chapter 7 Data Explorer Examples7-22 Applied Biosystems7Figure 7-22 Deisotoping Dialog Box10. For this example spectrum, specify H for Adduct and

8ChapterData Explorer™ Software User’s Guide 8-18 Viewing Voyager PSD DataThis chapter contains the following sections:8.1 Displaying PSD Data ...

Chapter 1 Data Explorer™ Basics1-20 Applied Biosystems1Opening,customizing, andsaving .SET filesTo open, customize, and save .SET files:1. If you

Chapter 8 Viewing Voyager PSD Data8-2 Applied Biosystems88.1 Displaying PSD DataThis section includes:• Displaying the composite spectrum• Advanc

Displaying PSD DataData Explorer™ Software User’s Guide 8-38Figure 8-1 PSD Spectrum in Data ExplorerAdvancingthrough segmenttracesTo advance through

Chapter 8 Viewing Voyager PSD Data8-4 Applied Biosystems8The PSD Processing dialog box is displayed (Figure 8-2) and lists all segments contained

Displaying PSD DataData Explorer™ Software User’s Guide 8-58NOTE: The entry number in the PSD Segment list above may not correspond to Segment number

Chapter 8 Viewing Voyager PSD Data8-6 Applied Biosystems8How thecompositespectrum isgeneratedThe software does the following to generate a composi

Displaying PSD DataData Explorer™ Software User’s Guide 8-78If you are performing an internal standard calibration, the software determines the consta

Chapter 8 Viewing Voyager PSD Data8-8 Applied Biosystems88.2 Applying Fragment LabelsOverview Use the Ion Fragmentation calculator to apply fragm

Applying Fragment LabelsData Explorer™ Software User’s Guide 8-982. In the Sequence text box, type the amino acid sequence of the compound. Use single

Chapter 8 Viewing Voyager PSD Data8-10 Applied Biosystems88.3 Calibrating a PSD SpectrumNOTE: Multi-point calibration yields higher mass accuracy

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-1188.3.1 Checking Peak DetectionChecking Before calibrating, check that peaks in all

Customizing the Data Explorer WindowData Explorer™ Software User’s Guide 1-211To use the Settings option:1. Select Settings from the File menu. 2. Sel

Chapter 8 Viewing Voyager PSD Data8-12 Applied Biosystems88.3.2 Calibrating This section includes:• Calibrating• Matching peaks automatically• Se

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-138Figure 8-5 PSD Processing Dialog Box with Calibration Tab Displayed4. Select a PS

Chapter 8 Viewing Voyager PSD Data8-14 Applied Biosystems8NOTE: If the calibration reference file is stored on a network drive, an error message m

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-158Matching peaksautomaticallyIf you want the software to compare observed masses in

Chapter 8 Viewing Voyager PSD Data8-16 Applied Biosystems8Selecting peaksmanuallyFor optimum mass accuracy, select peaks as described in “Selectin

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-1782. Do any of the following:• Click OK to accept the highlighted reference mass for

Chapter 8 Viewing Voyager PSD Data8-18 Applied Biosystems8Solving andplottingAfter matching peaks, click Solve and Plot. The calibration statistic

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-198Selectingcalibration peaksfor optimum massaccuracyTo improve calibration statistic

Chapter 8 Viewing Voyager PSD Data8-20 Applied Biosystems88.3.3 Creating PSD Calibration (.CAL) Files and Applying to Other Data FilesCreating PS

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-2188.3.4 Creating PSD Calibration Reference (.REF) FilesOverview You can manually cr

Chapter 1 Data Explorer™ Basics1-22 Applied Biosystems14. To remove a button from a toolbar, click-drag the button from the toolbar.NOTE: The Cust

Chapter 8 Viewing Voyager PSD Data8-22 Applied Biosystems8NOTE: This selection determines the mass type specified for the reference masses in the

Calibrating a PSD SpectrumData Explorer™ Software User’s Guide 8-2388.3.5 Changing the Precursor MassWhen to changeprecursor massWhen analyzing the c

Chapter 8 Viewing Voyager PSD Data8-24 Applied Biosystems8Changing If the precursor mass taken from the data file is not correct:1. Display the Se

9ChapterData Explorer™ Software User’s Guide 9-19 TroubleshootingThis chapter contains the following sections:9.1 Overview ...

Chapter 9 Troubleshooting9-2 Applied Biosystems99.1 OverviewThis section includes:• General troubleshooting• Processing, tools, and applications

General TroubleshootingData Explorer™ Software User’s Guide 9-399.2 General TroubleshootingTable 9-1 General Troubleshooting—Mariner and VoyagerSym

Chapter 9 Troubleshooting9-4 Applied Biosystems9M/z range in data files converted to centroid does not match m/z range in original data fileM/z ra

General TroubleshootingData Explorer™ Software User’s Guide 9-59Spectra labeled with spectrum numbers that do not correspond to the axisYou are viewin

Chapter 9 Troubleshooting9-6 Applied Biosystems99.3 Processing, Tools, and Applications TroubleshootingTable 9-4 Processing, Tools, and Applica

Processing, Tools, and Applications TroubleshootingData Explorer™ Software User’s Guide 9-79Results not saved for all traces in an overlaid traceOnly

Setting Graphic OptionsData Explorer™ Software User’s Guide 1-2311.5 Setting Graphic OptionsThis section includes:• Changing background color• Custom

Chapter 9 Troubleshooting9-8 Applied Biosystems9After Single-charge Conversion of multiply charged peaks, you see charge states other than 0 or 1P

Processing, Tools, and Applications TroubleshootingData Explorer™ Software User’s Guide 9-99Table 9-5 Processing, Tools, and Applications Troublesho

Chapter 9 Troubleshooting9-10 Applied Biosystems99.4 Calibration TroubleshootingTable 9-6 Calibration Troubleshooting—Mariner and VoyagerSympto

Calibration TroubleshootingData Explorer™ Software User’s Guide 9-119Calibration returns an invalid number of matchesWhen creating a reference mass li

Chapter 9 Troubleshooting9-12 Applied Biosystems9Table 9-7 Calibration Troubleshooting—Mariner OnlySymptom Possible Cause ActionMass Calibration

Calibration TroubleshootingData Explorer™ Software User’s Guide 9-139Table 9-8 Calibration Troubleshooting—Voyager OnlySymptom Possible Cause Action

Chapter 9 Troubleshooting9-14 Applied Biosystems99.5 Printing TroubleshootingTable 9-9 Printing Troubleshooting—Mariner and VoyagerSymptom Poss

Peak Detection and Labeling TroubleshootingData Explorer™ Software User’s Guide 9-1599.6 Peak Detection and Labeling TroubleshootingThis section incl

Chapter 9 Troubleshooting9-16 Applied Biosystems9Peaks are not detected or labeled(continued)Analyzing masses above 20,000 DaIncrease Mass Resolut

Peak Detection and Labeling TroubleshootingData Explorer™ Software User’s Guide 9-179Expected user label not displayedDelta X value includes more than

Chapter 1 Data Explorer™ Basics1-24 Applied Biosystems11.5.2 Customizing Graphic OptionsThis section includes:• Accessing graphic options• Settin

Chapter 9 Troubleshooting9-18 Applied Biosystems9Partially resolved peaks not detectedMass resolution set too high to detect average massDecrease

Peak Detection and Labeling TroubleshootingData Explorer™ Software User’s Guide 9-199Known isotope not labeled with charge stateCharge State peak labe

Chapter 9 Troubleshooting9-20 Applied Biosystems9Spectrum peaks not labeled with charge state when charge state labels are selectedMass of origina

Peak Detection and Labeling TroubleshootingData Explorer™ Software User’s Guide 9-219Spectrum peaks labeled with incorrect charge state when charge st

Chapter 9 Troubleshooting9-22 Applied Biosystems9

AAppendixData Explorer™ Software User’s Guide A-1A WarrantyApplied Biosystems supplies or recommends certain configurations of computer hardware, sof

Appendix A WarrantyA-2 Applied BiosystemsAnot warrant that the operation of the instrument or software will be uninterrupted or error free. Applie

Data Explorer™ Software User’s Guide A-3AWarrantieslimitationsTHE REMEDIES PROVIDED HEREIN ARE BUYER’S SOLE AND EXCLUSIVE REMEDIES. WITHOUT LIMITING T

Appendix A WarrantyA-4 Applied BiosystemsA

BAppendixData Explorer™ Software User’s Guide B-1B Overview of IsotopesThis appendix contains the following sections:B.1 Isotopes ...

Setting Graphic OptionsData Explorer™ Software User’s Guide 1-251Figure 1-4 Graphic Options Dialog Box—Graph Setup TabSetting colors You can set colo

Appendix B Overview of IsotopesB-2 Applied BiosystemsBB.1 IsotopesOverview Many elements in their natural state exist as one of several isotopes.

IsotopesData Explorer™ Software User’s Guide B-3BAs the number of carbon atoms in a compound increases, the possibility of the compound containing a 1

Appendix B Overview of IsotopesB-4 Applied BiosystemsBFigure B-3 Mass Spectrum of Angiotensin I at Resolution 3,000In compounds with more than 10

IsotopesData Explorer™ Software User’s Guide B-5BFigure B-4 Mass Spectrum of Angiotensin I at Resolution 1,000If isotopes cannot be resolved, the hig

Appendix B Overview of IsotopesB-6 Applied BiosystemsBB.2 Monoisotopic and Average MassesWhen isotopes are clearly resolved (Figure B-6), the mon

Monoisotopic and Average MassesData Explorer™ Software User’s Guide B-7BFigure B-7 Average MassAverage masscorresponds tocentroid of unresolved peak

Appendix B Overview of IsotopesB-8 Applied BiosystemsBB.3 Isotopes of Common ElementsTable B-1 lists the natural abundance of isotopes for some c

CAppendixData Explorer™ Software User’s Guide C-1C Data Explorer Toolbox (Visual Basic Macros)This appendix includes:C.1 Overview...

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-2 Applied BiosystemsCC.1 OverviewMacros provided The following toolbox of Visual Basic ma

Preparing Data Before Accessing MacrosData Explorer™ Software User’s Guide C-3CReferencesrequiredThe following references are selected by default in t

Table of Contentsiv Applied BiosystemsChapter 2 Using Chromatogram and Spectrum Windows2.1 Opening and Closing Data Files ...

Chapter 1 Data Explorer™ Basics1-26 Applied Biosystems1When you manually set colors, note:• Selections set to white (or line widths set to 0) may

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-4 Applied BiosystemsCC.3 Accessing the MacrosTo access the macros:1. Open the Data Explor

Using the Ladder Sequencing ToolboxData Explorer™ Software User’s Guide C-5CNOTE: If the modToolBoxPalette.Toolbox_Palette is not listed, you must imp

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-6 Applied BiosystemsC2. Enter the mass tolerance to apply to the analysis.3. Click Get Spe

Using the Ladder Sequencing ToolboxData Explorer™ Software User’s Guide C-7C7. Under Annotate Spectrum, select the types of labels you want displayed:

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-8 Applied BiosystemsCIf DNA or RNA is selected, the software:• Examines the spectrum in 27

Using the Peptide Fragmentation ToolboxData Explorer™ Software User’s Guide C-9CC.5 Using the Peptide Fragmentation ToolboxUse the Peptide Fragmentat

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-10 Applied BiosystemsC3. Add peaks to the peak list to be included in the calculation by t

Using the Peptide Fragmentation ToolboxData Explorer™ Software User’s Guide C-11C• y and b pairsLists peak pairs whose combined masses plus 1 Da add

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-12 Applied BiosystemsC2. If desired, click Label Immonium Ions.NOTE: Label immonium ions b

Using the Peptide Fragmentation ToolboxData Explorer™ Software User’s Guide C-13C5. Click Copy to Output Window Result Tab to copy results to the Resu

Setting Graphic OptionsData Explorer™ Software User’s Guide 1-271Setting datacursorsTo enable data cursors and set cursor labels and attributes:1. Sel

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-14 Applied BiosystemsC4. Click Find Correlation.Correlations for the selected peak are lis

Using the Polymer Analysis ToolboxData Explorer™ Software User’s Guide C-15CC.6 Using the Polymer Analysis ToolboxUse the Polymer Analysis Toolbox to

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-16 Applied BiosystemsC3. Select the mode for the analysis:• Use the entire mass range—Calc

Using the Polymer Analysis ToolboxData Explorer™ Software User’s Guide C-17C• Use labeled peaks—Calculates average molecular weights using areas of pe

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-18 Applied BiosystemsCC.7 Using MS Fit/MS Tag ToolboxUse the MS Fit/MS Tag toolbox when a

Using MS Fit/MS Tag ToolboxData Explorer™ Software User’s Guide C-19C2. Click:• MS-Fit tabIf you are examining peptide data from a protein digest.• M

Appendix C Data Explorer Toolbox (Visual Basic Macros)C-20 Applied BiosystemsC

Data Explorer Software User’s Guide Index-1IndexIDEXNNumerics and Symbols- in spectrum header 2-31%Base Peak Intensitydefinition, chromatogram 3-20def

IDEXNIndex-2 Applied BiosystemsAmino acids, labeling C-5Analog signal, displaying 4-2Analyzer Temperature, displaying trace 4-2ANGIOTENSIN_FRAGMENTS.R

Data Explorer Software User’s Guide Index-3IDEXNBar mode, traces 1-28BAS files for macros 6-43Base mass, labeling peaks 3-55, 3-56Base peak intensityd

Chapter 1 Data Explorer™ Basics1-28 Applied Biosystems1Setting traces inLine or VerticalBar modeYou can change the trace display from Line to Vert

IDEXNIndex-4 Applied BiosystemsCalibrating mass, automatic (Mariner data only) (continued)reverting to instrument calibration 5-22troubleshooting 9-9t

Data Explorer Software User’s Guide Index-5IDEXNCalibration constantssee also Calibrating massapplying to new file 5-16, 8-20calculating 5-34displayed

IDEXNIndex-6 Applied BiosystemsCharge state, peak (continued)requirements for labeling 3-53single 5-59tolerance calculation 3-32troubleshooting 9-17z

Data Explorer Software User’s Guide Index-7IDEXNCombiSolv datadisplaying one injection 4-24Event Tag Filtering command dimmed (Mariner data only) 4-24

IDEXNIndex-8 Applied BiosystemsCustomizing (continued)SET files 1-17toolbars 1-22DDADdisplaying Channels 1-12, 4-2displaying TAC 1-12displaying traces

Data Explorer Software User’s Guide Index-9IDEXNData file (continued)full name not displayed 1-14inserting traces into 2-37moving between open 2-8mult

IDEXNIndex-10 Applied BiosystemsDetection Ranges (continued)setting manually, chromatogram 3-19, 3-20setting manually, spectrum 3-28setting parameters

Data Explorer Software User’s Guide Index-11IDEXNExcel, see Microsoft ExcelExiting software 1-3Expanding traces 2-21Exportingsee also ConvertingASCII

IDEXNIndex-12 Applied BiosystemsFilter Width Incrementsetting manually, spectrum 3-31suggested value, spectrum 3-31value used when resolution-based pe

Data Explorer Software User’s Guide Index-13IDEXNIImmonium ions, labeling C-9IMMONIUM_IONS.REF 5-18, 8-19Import Calibrationerror displayed 9-11, 9-12p

Setting Graphic OptionsData Explorer™ Software User’s Guide 1-2911.5.3 Reverting to Previous Graphic OptionsYou have two options to revert to previou

IDEXNIndex-14 Applied BiosystemsIsotope Match Intensity, elemental targeting 6-33Isotope Match Scoreelemental composition 6-6elemental composition, no

Data Explorer Software User’s Guide Index-15IDEXNMMacro Recorderadvanced editing 6-42buttons, assigning to macros 6-38DATAEXPLORER.VB6 location 6-35DA

IDEXNIndex-16 Applied BiosystemsMass Calibration commandsdimmed on menu 9-11not displayed on menu 9-8Mass calibration, see Calibrating massMass, centr

Data Explorer Software User’s Guide Index-17IDEXNMS Method (Mariner data only) (continued)instrument settings, viewing 4-23spectrum numbers in filtere

IDEXNIndex-18 Applied BiosystemsOutput windowacquisition comment, displaying 1-15calibration statistics, displaying 5-13, 8-18Chro Peak list tab 1-15c

Data Explorer Software User’s Guide Index-19IDEXNPeak detection (continued)Noise Threshold, calculated automatically for chromatogram data 3-21, 3-68o

IDEXNIndex-20 Applied BiosystemsPeak labels (continued)centroid 3-56chromatogram, setting 3-54custom 3-61custom, creating for fragment spectra 8-9cust

Data Explorer Software User’s Guide Index-21IDEXNPeak weighting factors 5-10, 8-14Peak Widthminimum and maximum used 3-21, 3-25set automatically by so

IDEXNIndex-22 Applied BiosystemsPSD analysis (continued)composite spectrum, displaying 8-2, 8-5composite spectrum, how it is generated 8-6fragment lab

Data Explorer Software User’s Guide Index-23IDEXNResult tab, Output window 1-15Resultssee also RSD and RCDannotating traces with 2-28copying 2-28displ

Chapter 1 Data Explorer™ Basics1-30 Applied Biosystems11.6 Managing FilesThis section describes:• Converting .SPC file format to .DAT file format

IDEXNIndex-24 Applied BiosystemsSequence Control Panel, Mariner, automatic calibration settings (reference masses) for 5-27Sequence Control Panel, Voy

Data Explorer Software User’s Guide Index-25IDEXNSpectra (continued)summing non-contiguous 4-21troubleshooting 9-17truncating 5-56types of 5-2Spectrum

IDEXNIndex-26 Applied BiosystemsTTabsfor open files 2-8in Data Explorer window 2-8TACin chromatogram header 2-30Mariner data, optional 1-12Tag, see Ev

Data Explorer Software User’s Guide Index-27IDEXNTraces (continued)Replace mode, setting 2-17scaling mode, setting 2-12splitting 2-15switching between

IDEXNIndex-28 Applied BiosystemsVValley-to-Baseline integrationchromatogram 3-21, 3-70spectrum 3-26, 3-70Valley-to-Valley integrationchromatogram 3-21

Data Explorer Software User’s Guide Index-29IDEXNXX cursors, setting 1-27x,y data pairs, copying 1-39XACin chromatogram header 2-30see also Extracted

IDEXNIndex-30 Applied Biosystems

Headquarters850 Lincoln Centre DriveFoster City, CA 94404 USAPhone: +1 650.638.5800Toll Free (In North America): +1 800.345.5224Fax: +1 650.638.5884Wo

Managing FilesData Explorer™ Software User’s Guide 1-311Before you begin Confirm that the .SPC and .CGM files are located in the same directory. Use W

Chapter 1 Data Explorer™ Basics1-32 Applied Biosystems1The Convert to .DAT Format dialog box reappears.5. Click OK. A message box is displayed, sh

Managing FilesData Explorer™ Software User’s Guide 1-3311.6.2 Converting Data from Profile to Centroid (Mariner Data Only)Overview You can convert an

Chapter 1 Data Explorer™ Basics1-34 Applied Biosystems11.6.3 Converting to and Exporting ASCII Data This section describes:• Converting a data fi

Managing FilesData Explorer™ Software User’s Guide 1-3511.6.4 Importing a Trace in ASCII FormatYou can import trace data in ASCII format. If the file

Table of Contents Data Explorer™ Software User’s Guide vChapter 3 Peak Detection and Labeling3.1 Overview ...

Chapter 1 Data Explorer™ Basics1-36 Applied Biosystems1CAUTIONAn imported ASCII format trace contains only the data points for the trace. The Samp

Managing FilesData Explorer™ Software User’s Guide 1-371NOTE: To export calibration constants used to acquire the data, select Mass Calibration from t

Chapter 1 Data Explorer™ Basics1-38 Applied Biosystems1Saving .LBSand .LBC filesTo save spectrum (.LBS) or chromatogram (.LBC) peak label files fr

Managing FilesData Explorer™ Software User’s Guide 1-391NOTE: If you paste the image into an application that does not handle Windows Metafile format

Chapter 1 Data Explorer™ Basics1-40 Applied Biosystems1NOTE: Copy Displayed Peaks copies all fields and headings. However, some data applications

Managing FilesData Explorer™ Software User’s Guide 1-4112. Select the trace window to copy. 3. Display the peak list by selecting Output Window from t

Chapter 1 Data Explorer™ Basics1-42 Applied Biosystems1

2ChapterData Explorer™ Software User’s Guide 2-12 Using Chromatogram and Spectrum WindowsThis chapter contains the following sections:2.1 Opening an

Chapter 2 Using Chromatogram and Spectrum Windows2-2 Applied Biosystems22.1 Opening and Closing Data FilesThis section includes:• Opening data fi

Opening and Closing Data FilesData Explorer™ Software User’s Guide 2-32.Figure 2-1 Select Files Dialog Box2. Click the down arrow to display the File

Table of Contentsvi Applied BiosystemsChapter 4 Examining Chromatogram Data4.1 Overview ...

Chapter 2 Using Chromatogram and Spectrum Windows2-4 Applied Biosystems2Specifying settings 5. Select a Restoring Graphics and Processing Settings

Opening and Closing Data FilesData Explorer™ Software User’s Guide 2-52Figure 2-2 Data Explorer Window with Four Mariner Data Files Open (Each .DAT F

Chapter 2 Using Chromatogram and Spectrum Windows2-6 Applied Biosystems2The data is labeled accordingly:Automaticallyrunning macrosYou can set mac

Opening and Closing Data FilesData Explorer™ Software User’s Guide 2-722.1.3 Displaying Voyager ChromatogramsTo display chromatograms for multispectr

Chapter 2 Using Chromatogram and Spectrum Windows2-8 Applied Biosystems22.1.5 Moving Between Open FilesYou can have more than one file open at a

Opening and Closing Data FilesData Explorer™ Software User’s Guide 2-92Figure 2-5 Select File to Activate Dialog Box3. Select:• Maximize—To maximize

Chapter 2 Using Chromatogram and Spectrum Windows2-10 Applied Biosystems22.1.6 Closing Data FilesYou can close files in the following ways:• Sele

Adjusting the Display RangeData Explorer™ Software User’s Guide 2-1122.2 Adjusting the Display RangeTo set the display range:1. Click the Chromatogra

Chapter 2 Using Chromatogram and Spectrum Windows2-12 Applied Biosystems25. Set the parameters described below as needed:6. Click OK.Parameter Des

Organizing WindowsData Explorer™ Software User’s Guide 2-1322.3 Organizing WindowsLinking views Linking Chromatogram or Spectrum windows in different

Table of Contents Data Explorer™ Software User’s Guide vii5.5 Centroiding ...

Chapter 2 Using Chromatogram and Spectrum Windows2-14 Applied Biosystems22.4 Manipulating TracesThis section includes:• Zooming centering, and cu

Manipulating TracesData Explorer™ Software User’s Guide 2-152Centering a peakin the traceTo center a peak in the trace window:1. Display the trace con

Chapter 2 Using Chromatogram and Spectrum Windows2-16 Applied Biosystems2For example, if you select Divide Active Trace to Four when the active tr

Manipulating TracesData Explorer™ Software User’s Guide 2-172When you perform certain functions (for example, smoothing), a new trace is created. You

Chapter 2 Using Chromatogram and Spectrum Windows2-18 Applied Biosystems22. Select the Replace Mode:• Replace the Active Trace (default)—Replaces

Manipulating TracesData Explorer™ Software User’s Guide 2-192Figure 2-8 Adding Traces (Four Traces Shown, up to Four More Can Be Added)When you perfo

Chapter 2 Using Chromatogram and Spectrum Windows2-20 Applied Biosystems2Figure 2-9 shows the original trace and three added traces that now conta

Manipulating TracesData Explorer™ Software User’s Guide 2-2122.4.5 Removing TracesRemoving theactive traceTo remove the active trace from a window:1.

Chapter 2 Using Chromatogram and Spectrum Windows2-22 Applied Biosystems22.4.7 Recalling and Rearranging Traces (Processing History)Overview The

Manipulating TracesData Explorer™ Software User’s Guide 2-232SettingProcessingHistory optionsTo set Processing History options:1. From the Tools menu,

Table of Contentsviii Applied BiosystemsChapter 7 Data Explorer Examples7.1 Mariner Data Examples ...

Chapter 2 Using Chromatogram and Spectrum Windows2-24 Applied Biosystems22.4.8 Overlaying TracesThis section includes:• Overlaying traces from di

Manipulating TracesData Explorer™ Software User’s Guide 2-252NOTE: When saving results, only the results for the active trace are saved.Overlaying tra

Chapter 2 Using Chromatogram and Spectrum Windows2-26 Applied Biosystems2Changing theactive traceTo change the active trace in an overlay:1. From

Manipulating TracesData Explorer™ Software User’s Guide 2-272NOTE: You must select the Use same settings for all traces check box before selecting opt

Chapter 2 Using Chromatogram and Spectrum Windows2-28 Applied Biosystems22.4.9 Annotating TracesYou can add text annotation to traces by:• Copyin

Manipulating TracesData Explorer™ Software User’s Guide 2-292Annotating thetraceTo annotate the trace:1. Click the trace at the location where you wan

Chapter 2 Using Chromatogram and Spectrum Windows2-30 Applied Biosystems22.4.10 Viewing Trace LabelsThe Data Explorer software includes a label i

Manipulating TracesData Explorer™ Software User’s Guide 2-312Figure 2-11 illustrates an extracted ion chromatogram with a “XIC” chromatogram trace lab

Chapter 2 Using Chromatogram and Spectrum Windows2-32 Applied Biosystems2BPI Base peak intensityCT CentroidDAD Diode array dataDECONV (Mariner da

Manipulating TracesData Explorer™ Software User’s Guide 2-332Figure 2-12 illustrates a smoothed spectrum with an “SM5” spectrum trace label.Figure 2-1

Table of Contents Data Explorer™ Software User’s Guide ixAppendix A Warranty Information... A-1Appendix B Overvie

Chapter 2 Using Chromatogram and Spectrum Windows2-34 Applied Biosystems23. To print with the x-axis along the longest length of the paper, select

Manipulating TracesData Explorer™ Software User’s Guide 2-352NOTE: Line Widths of 0 or 1 (or lines set to the color white) may not print on certain pr

Chapter 2 Using Chromatogram and Spectrum Windows2-36 Applied Biosystems22.5 Working with Multiple Data FilesWhen you have multiple data files op

Working with Multiple Data FilesData Explorer™ Software User’s Guide 2-372NOTE: If you select Print All Views when more than two data files are open,

Chapter 2 Using Chromatogram and Spectrum Windows2-38 Applied Biosystems2Comparingcopied tracesAfter you copy a trace to another trace window, you

Exporting, Opening, and Deleting .RCD and .RSD Results Files (Mariner Data Only)Data Explorer™ Software User’s Guide 2-3922.7 Exporting, Opening, and

Chapter 2 Using Chromatogram and Spectrum Windows2-40 Applied Biosystems2Deleting resultsfor .RCD and .RSDfilesUse Windows NT Explorer to delete .

Saving, Opening, and Deleting .SPC Results Files (Mariner Data Only)Data Explorer™ Software User’s Guide 2-4123. Select the .RST or .RCT file to open,

Chapter 2 Using Chromatogram and Spectrum Windows2-42 Applied Biosystems2

3ChapterData Explorer™ Software User’s Guide 3-13 Peak Detection and LabelingThis chapter contains the following sections:3.1 Overview ....