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OpenSwathChromatogramExtractor

Extracts chromatograms (XICs) from a file containing spectra.

potential predecessor tools $ \longrightarrow $ OpenSwathChromatogramExtractor $ \longrightarrow $ potential successor tools
FileFilter OpenSwathAnalyzer

This module extracts ion traces (extracted ion chromatograms or XICs) from a file containing spectra. The masses at which the chromatograms should be extracted are stored in a TraML file and the result is stored in a mzML file holding chromatograms. This tool is designed to extract chromatogams from SWATH (data independent acquisition) data (see ref[1]), thus it will extract the masses found in the product ion section of the TraML transitions, returning as many chromatograms as input transitions were provided.

For SWATH data, the "is_swath" flag which will check the precursor isolation window of the first scan and assume all scans in that file were recorded with this precursor window (thus making it necessary to provide one input file per SWATH window). The module will then only extract transitions whose precursors fall into the corresponding isolation window.

For the extraction method, two convolution functions are available: top-hat and bartlett. While top-hat will just sum up the signal within a quadratic window, bartlett will weigh the signal in the center of the window more than the signal on the edge.

[1] Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717.

The command line parameters of this tool are:

The algorithm parameters for the Analyzer filter are:


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Jan 27 2016 17:15:21 using doxygen 1.8.10