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required parameter

advanced parameter

+TMTAnalyzerCalculates TMT quantitative values for peptides

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

++1Instance '1' section for 'TMTAnalyzer'

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[126:liver, 131:lung] Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format :, e.g. "114:myref","115:liver".

++++Quantification

isotope_correctionfalse Enable isotope correction (highly recommended). Note that you need to provide a correction matrix (see isotope_correction:tmt-6plex otherwise the tool will fail.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_reference126 Number of the reference channel (126-131).126:131

+++++isotope_correctionIsotope correction matrices for tmt-6plex.

tmt-6plex[126:0/0/0/0, 127:0/0/0/0, 128:0/0/0/0, 129:0/0/0/0, 130:0/0/0/0, 131:0/0/0/0] Override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'.

++++MetaInformation

ProgramOpenMS::TMTAnalyzer