OpenMS
2.6.0
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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).
The command line parameters of this tool are:
InclusionExclusionListCreator -- Creates inclusion and/or exclusion lists. Full documentation: http://www.openms.de/documentation/TOPP_InclusionExclusionListCreator.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. Usage: InclusionExclusionListCreator <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 '*'): -include <file> Inclusion list input file in FASTA or featureXML format. (valid formats: 'feat ureXML', 'fasta') -exclude <file> Exclusion list input file in featureXML, idXML or FASTA format. (valid formats : 'featureXML', 'idXML', 'fasta') -out <file>* Output file (tab delimited csv file). (valid formats: 'csv') -rt_model <file> RTModel file used for the rt prediction of peptides in FASTA files. (valid formats: 'txt') -pt_model <file> PTModel file used for the pt prediction of peptides in FASTA files (only neede d for inclusion_strategy PreotinBased_LP). (valid formats: 'txt') -inclusion_charges <charge> List containing the charge states to be considered for the inclusion list comp ounds, space separated. (min: '1') -inclusion_strategy <name> Strategy to be used for selection (default: 'ALL' valid: 'FeatureBased_LP', 'ProteinBased_LP', 'ALL') -exclusion_charges <charge> List containing the charge states to be considered for the exclusion list comp ounds (for idXML and FASTA input), space separated. (min: '1') -raw_data <mzMLFile> File containing the raw data (only needed for FeatureBased_LP). (valid formats : 'mzML') 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 --help Shows options --helphelp Shows all options (including advanced) The following configuration subsections are valid: - algorithm Inclusion/Exclusion algorithm 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. For more information, please consult the online documentation for this tool: - http://www.openms.de/documentation/TOPP_InclusionExclusionListCreator.html
INI file documentation of this tool: