Overview 

LabKey currently provides two MS1 Pipelines:

  • Pipeline #1:  msInspect Find Features
    • peakaboo peak finding
    • msInspect feature finding
  • Pipeline #2 : msInspect Find Features and Match Peptides
    • peakaboo peak finding
    • msInspect feature finding
    • pepmatch MS1 feature-MS2 peptide linking

For information on how to download and build peakaboo and pepmatch, please view this documentation.

Each pipeline makes use of Tasks.  These currently include:

  • peakaboo
  • msInspect
  • pepmatch

Pipeline #1:  Find MS1 Features

  • Button: msInspect Find Features
  • Protocol Folder: inspect
  • Initial type: .mzXML
  • Output type: .features.tsv (.peaks.xml)

Flow Diagram: msInspect Feature Finding Analysis



Flow Diagram: msInspect Feature Finding Analysis with Peakaboo peaks analysis

Pipeline #2: Match MS1 Features to Peptides

  • Button: msInspect Find Features and Match Peptides
  • Protocol Folder: ms1peptides
  • Initial type: .pep.xml
  • Output type: .peptides.tsv (.peaks.xml)

Flow Diagram: msInspect Feature Peptide Matching Analysis



Flow Diagram: msInspect Feature Peptide Matching with Peakaboo peaks Analysis

Task:  peakaboo (not included in default installation)

Extensions:
inputExtension = .mzXML
outputExtension = .peaks.xml

Usage:
peakaboo [options] [files]+

ParameterArgumentsDescriptionCommand Line Help
pipeline, peakaboo enabled Enables/disables Peakaboo execution as part of pipeline. Values are true/false. Defaults to true. 
pipeline, import peaks Skips importing peak data into the database. Values are true/false. Defaults to true. 
peakaboo, start scan--scanBegin arg (=1)Minimum scan number (default 1). beginning scan
peakaboo, end scan--scanEnd arg (=2147483647)Maximum scan number (default last). ending scan
peakaboo, minimum m/z--mzLow arg (=200)Minimum M/Z value (default:  the minimum m/z value in the file).  set mz low cutoffset mz low cutoff
peakaboo, maximum m/z--mzHigh arg (=2000)Maximum M/Z value (default:  the maximum m/z value in the file). set mz high cutoff

 

Example:

<?xml version="1.0"?>
<bioml>
<note type="input" label="peakaboo, minimum m/z">100</note>
<note type="input" label="peakaboo, maximum m/z">300</note>
</bioml>

Task:  msInspect

Extensions:
inputExtension = .mzXML
outputExtension = .features.tsv

Usage:
--findPeptides [--dumpWindow=windowSize] [--out=outfilename] [--outdir=outdirpath] [--start=startScan][--count=scanCount] [--minMz=minMzVal] [--maxMz=maxMzVal] [--strategy=className] [--noAccurateMass] [--accurateMassScans=<int>]
[--walkSmoothed] mzxmlfile

Details:
The findpeptides command finds peptide features in an mzXML file, based on the criteria supplied

Argument Details:  ('*' indicates a required parameter)
        *(unnamed ...): Input mzXML file(s)
 

ParameterArgumentDescription
msinspect findpeptides, start scanstartMinimum scan number (default 1)
msinspect findpeptides, scan countcountNumber of scans to search, if not all (default 2147483647)
msinspect findpeptides, minimum m/zminmzMinimum M/Z Value (default: the minimum m/z value in the file)
msinspect findpeptides, maximum m/zmaxmzMaximum M/Z Value (default: the maximum m/z value in the file)
msinspect findpeptides, strategystrategyClass name of a feature-finding strategy implementation
msinspect findpeptides, accurate mass scansaccuratemassscansWhen attempting to improve mass-accuracy, consider a neighborhood of <int> scans (default 3)
msinspect findpeptides, no accurate massnoaccuratemassDo not attempt mass-accuracy adjustment after default peak finding strategy (default false)
msinspect findpeptides, walk smoothedwalksmoothedWhen calculating feature extents, use smoothed rather than wavelet-transformed spectra) (default false) 

Example:

<?xml version="1.0"?>
<bioml>
<note type="input" label="msinspect findpeptides, minimum m/z">100</note>
<note type="input" label="msinspect findpeptides, maximum m/z">300</note>
</bioml>

Task: pepmatch

Extensions:
inputExtension = .features.tsv
outputExtension = .peptides.tsv

Usage:
pepmatch <pepXML file> <feature file> [options]

ParameterArgumentsDescriptionCommand Line Help
ms1 pepmatch, window-w<window>Filters on the specificed mz-delta window (default 1.0)filters on the specified mz-delta window.
ms1 pepmatch, min probability-p<min>Minimum Peptide Prophet probability to match.  Min = 0.0.  Max = 1.0minimum PeptideProphet probability to match.
ms1 pepmatch, require match charge-cDiscard matches where pepXML assumed charge does not match MS1 data (values are true/false)discard matches where pepXML assumed charge does not match MS1 data

Example:

<?xml version="1.0"?>
<bioml>
<note type="input" label="ms1 pepmatch, require match charge">true</note>
</bioml>

 

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