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PrecursorIonSelector

A tool for precursor ion selection based on identification results.

pot. predecessor tools → PrecursorIonSelector → pot. successor tools
FeatureFinderCentroided -

This tool provides a precursor ion selection based on previous MS/MS identifications.

Different strategies can be chosen:

DEX Dynamic exclusion of features with m/z matching predicted tryptic peptides masses of already identified proteins.
SPS Selection based on score reflecting the feature's suitability for fragmentation.
Downshift Similar to DEX, but features are not excluded, only ranked down in the feature list
Upshift Features with m/z matching predicted tryptic peptide masses of unidentified proteins are ranked up.
IPS Combination of Down- and Upshift.
ILP_IPS Iterative precursor ion selection using LP formulations.

This method is described in: Zerck, A. and Nordhoff, E. and Resemann, A. and Mirgorodskaya, E. and Suckau, D. and Reinert, K. and Lehrach, H. and Gobom, J.: An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics, J Prot Res, 2009, 8 (7), 3239-3251.

Given the feature map of the LC-MS run and the identification results the tool determines the next precursors. The precursors are ranked depending on the chosen strategy.

It is also possible run a simulation of selection strategies on a complete LC-MS/MS run, e.g. to determine what would have been the most efficient strategy.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:

For the parameters of the algorithm section see the algorithm's documentation:
OpenMS::PrecursorIonSelection