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TMTAnalyzer

Extracts and normalizes TMT information from an MS experiment.

pot. predecessor tools $ \longrightarrow $ TMTAnalyzer $ \longrightarrow $ pot. successor tools
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Extract the TMT reporter ion intensities (6plex) from raw MS2 data, does isotope corrections and stores the resulting quantitation as consensusXML, where each consensus centroid corresponds to one TMT MS2 scan (e.g., CID). The position of the centroid is the precursor position, its sub-elements are the channels (thus having m/z's of 126-131).

Isotope correction is done using non-negative least squares (NNLS). See ITRAQAnalyzer for details.

The correction matrices can be found (and changed) in the INI file. However, these matrices for TMT 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:

INI file documentation of this tool:


OpenMS / TOPP release 2.1.0 Documentation generated on Sat Apr 8 2017 21:05:40 using doxygen 1.8.13