Extracts chromatograms (XICs) from a file containing spectra.
| potential predecessor tools |  OpenSwathChromatogramExtractor | 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 chromatograms 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:
OpenSwathChromatogramExtractor -- Extract chromatograms (XIC) from a MS2 map file.
Version: 2.3.0 Jan 9 2018, 17:46:23, Revision: 38ae115
Usage:
OpenSwathChromatogramExtractor <options>
Options (mandatory options marked with '*'):
-in <files>* Input files separated by blank (valid formats: 'mzML')
-tr <file>* Transition file ('TraML' or 'csv') (valid formats: 'csv', 'traML')
-rt_norm <file> RT normalization file (how to map the RTs of this run to the ones stored in
the library) (valid formats: 'trafoXML')
-out <file>* Output file (valid formats: 'mzML')
-min_upper_edge_dist <double> Minimal distance to the edge to still consider a precursor, in Thomson (defa
ult: '0')
-mz_window <double> Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag).
This is the full window size, e.g. 100 ppm would extract 50 ppm on either
side. (default: '0.05' min: '0')
-rt_window <double> Extraction window in RT dimension (-1 means extract over the whole range).
This is the full window size, e.g. a value of 1000 seconds would extract
500 seconds on either side. (default: '-1')
-is_swath Set this flag if the data is SWATH data
-ppm M/z extraction_window is in ppm
-extract_MS1 Extract the MS1 transitions based on the precursor values in the TraML file
-extraction_function <name> Function used to extract the signal (default: 'tophat' valid: 'tophat', 'bar
tlett')
Options to control the modeling of retention time transformations from data:
-model:type <name> Type of model (default: 'linear' valid: 'linear', 'b_spline', 'interpolated'
, 'lowess')
-model:symmetric_regression Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x',
instead of on 'y' vs. 'x'.
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default:
'1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
The algorithm parameters for the Analyzer filter are: