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InclusionExclusionListCreator

A tool for creating inclusion and/or exclusion lists for LC-MS/MS.

potential predecessor tools → InclusionExclusionListCreator → potential successor tools
MascotAdapter (or other ID engines) -
FeatureFinderCentroided

Currently this tool can create tab-delimited inclusion or exclusion lists (m/z, RT start, RT stop). The input can either be peptide identifications from previous runs, a feature map or a FASTA-file with proteins. Inclusion and exclusion charges can be specified for FASTA and idXML input. If no charges are specified in the case of peptide id input, only the charge state of the peptide id is in/excluded, otherwise all given charge states are entered to the list.

InclusionExclusionListCreator has different strategies for inclusion list creation: 'FeatureBased_LP', 'ProteinBased_LP' and 'ALL'. In the ALL mode all features are put onto the list. The FeatureBased_LP, which was designed for MALDI data, maximizes the number of features in the inclusion list given the constraints that for each RT fraction a maximal number of precursors is not exceeded and each feature is scheduled at most a fixed number of times. In this mode, the sum of normalized feature intensities is maximized so that for each feature high intensity RTs are favoured over lower intensity ones. The ProteinBased_LP uses RT and detectability prediction methods to predict features that are most likely to be identified by MS/MS. Both LP methods are described in more detail in a recent publication: Zerck et al.: Optimal precursor ion selection for LC-MALDI MS/MS (BMC Bioinformatics 2013).

The RT window size can be specified in the RT section of the INI file, either as relative window with [rt-rel_rt_window_size*rt,rt+rel_rt_window_size*rt] or absolute window.

The default is RT in minutes, but seconds can also be used (see INI file).

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: