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MS1 Pipelines

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MS1 Pipelines

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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]+

Parameter Arguments Description Command 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 cutoff set 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)
 

Parameter Argument Description
msinspect findpeptides, start scan start Minimum scan number (default 1)
msinspect findpeptides, scan count count Number of scans to search, if not all (default 2147483647)
msinspect findpeptides, minimum m/z minmz Minimum M/Z Value (default: the minimum m/z value in the file)
msinspect findpeptides, maximum m/z maxmz Maximum M/Z Value (default: the maximum m/z value in the file)
msinspect findpeptides, strategy strategy Class name of a feature-finding strategy implementation
msinspect findpeptides, accurate mass scans accuratemassscans When attempting to improve mass-accuracy, consider a neighborhood of <int> scans (default 3)
msinspect findpeptides, no accurate mass noaccuratemass Do not attempt mass-accuracy adjustment after default peak finding strategy (default false)
msinspect findpeptides, walk smoothed walksmoothed When 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]

Parameter Arguments Description Command 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 = 1.0 minimum PeptideProphet probability to match.
ms1 pepmatch, require match charge -c Discard 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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