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OpenMS
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A tool for precursor ion selection based on identification results.
pot. predecessor tools | → PrecursorIonSelector → | pot. successor tools |
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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.
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