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ITRAQAnalyzer

Extracts and normalizes iTRAQ information from an MS experiment.

pot. predecessor tools $ \longrightarrow $ ITRAQAnalyzer $ \longrightarrow $ pot. successor tools
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Extract the iTRAQ reporter ion intensities (4plex or 8plex) from raw MS2 data, does isotope corrections and stores the resulting quantitation as consensusXML, where each consensus centroid corresponds to one iTRAQ MS2 scan (e.g., HCD). The position of the centroid is the precursor position, its sub-elements are the channels (thus having m/z's of 113-121).

Isotope correction is done using non-negative least squares (NNLS), i.e.,

Minimize ||Ax - b||, subject to x >= 0, where b is the vector of observed reporter intensities (with 'contaminating' isotope species), A is a correction matrix (as supplied by the manufacturer AB Sciex) and x is the desired vector of corrected (real) reporter intensities. Other software solves this problem using an inverse matrix multiplication, but this can yield entries in x which are negative. In a real sample, this solution cannot possibly be true, so usually negative values (= negative reporter intensities) are set to 0. However, a negative result usually means, that noise was not accounted for thus we use NNLS to get a non-negative solution, without the need to truncate negative values. In (the usual) case that inverse matrix multiplication yields only positive values, our NNLS will give the exact same optimal solution.

The correction matrices can be found (and changed) in the INI file. However, these matrices for both 4plex and 8plex are now stable, and every kit delivered should have the same isotope correction values. Thus, there should be no need to change them, but feel free to compare the values in the INI file with your kit's Certificate.

After this quantitation step, you might want to annotate the consensus elements with the respective identifications, obtained from an identification pipeline. Note that quantification is solely on peptide level at this stage. In order to obtain protein quantifications, you can try TextExporter to obtain a simple text format which you can feed to other software tools (e.g., R), or you can try ProteinQuantifier.

The command line parameters of this tool are:

ITRAQAnalyzer -- Calculates iTRAQ quantitative values for peptides
Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND

Usage:
  ITRAQAnalyzer <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

Options (mandatory options marked with '*'):
  -type <mode>       ITRAQ experiment type
                     (default: '4plex' valid: '4plex', '8plex')
  -in <file>*        Input raw/picked data file  (valid formats: 'mzML')
  -out <file>*       Output consensusXML file with quantitative information (valid formats: 'consensusXML')
  -out_stats <file>  Output statistics as tab-separated file (readable by R or Excel or ...) (valid formats: 
                     'tsv')
                     
                     
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
  -id_pool <file>    ID pool file to DocumentID's for all generated output files. Disabled by default. (Set 
                     to 'main' to use /builddir/build/BUILD/OpenMS-88dc253b95db54419bd484ffb07697193491484b/s
                     hare/OpenMS/IDPool/IDPool.txt)
  --help             Shows options
  --helphelp         Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+ITRAQAnalyzerCalculates iTRAQ quantitative values for peptides
version2.0.0 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
forcefalse Overwrite tool specific checks.true,false
id_pool ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /builddir/build/BUILD/OpenMS-88dc253b95db54419bd484ffb07697193491484b/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

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:31 using doxygen 1.8.9.1