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required parameter

advanced parameter

+ITRAQAnalyzerCalculates iTRAQ quantitative values for peptides

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ITRAQAnalyzer'

type4plex iTRAQ experiment type
4plex,8plex

in input raw/picked data file input file*.mzML

out output consensusXML file with quantitative informationoutput file*.consensusXML

out_mzq Optional output file of MzQuantML.output file*.mzq

out_stats output statistics as tab-separated file (readable by R or Excel or ...)output file*.tsv

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

id_pool ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /group/agabi/OpenMS/nightly-builds/RELEASE_BRANCH/share/OpenMS/IDPool/IDPool.txt)

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmAlgorithm parameters section

++++Extraction

select_activationHigh-energy collision-induced dissociation Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering.Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,

reporter_mass_shift0.1 Allowed shift (left to right) in Da from the expected position.1e-08:0.5

channel_active[114:liver, 117:lung] Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format :, e.g. "114:myref","115:liver".

++++Quantification

isotope_correctiontrue Enable isotope correction (highly recommended).true,false

do_normalizationfalse Normalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!true,false

channel_reference114 Number of the reference channel (114-117 for 4plex).114:117

+++++isotope_correctionIsotope correction matrices for 4plex and 8plex. Only one of them will be used (depending on iTRAQ mode).

4plex[114:0/1/5.9/0.2, 115:0/2/5.6/0.1, 116:0/3/4.5/0.1, 117:0.1/4/3.5/0.1] Override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'.

8plex[113:0/0/6.89/0.22, 114:0/0.94/5.9/0.16, 115:0/1.88/4.9/0.1, 116:0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0, 118:0.09/4.71/1.88/0, 119:0.14/5.66/0.87/0, 121:0.27/7.44/0.18/0] Override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'.

++++MetaInformation

ProgramOpenMS::ITRAQAnalyzer