OpenMS
2.5.0
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This could be merged in the future with the general IDMergerAlgorithm since it shares a lot. IDMergerAlgorithm needs additional methods to have multiple runs as output. It also needs to store an extended mapping internally to distribute the PeptideIDs to the right output run according to origin and label. And should have non-copying/moving overloads for inserting PeptideIDs since we probably do not want to distribute the PeptideIDs to the features again. In general detaching IDs from features would be of great help here.
Untested for TMT/iTraq data where you usually have one Identification run per File but in one File you might have multiple conditions multiplexed, that you might want to split for inference. Problem: There is only one PeptideIdentification object per Feature that is representative for all "submaps" (in this case the labels/reporter ions). -> A lookup is necessary if the reporter ion had non-zero intensity and if so, the peptide ID needs to be duplicated for every new (condition-based) IdentificationRun it is supposed to be used in, according to the mapping.
Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc)
Implement user-specified seed lists support (Marc)
Implement reading of pepXML and protXML (Andreas)
Allow reading of zipped XML files (David, Hiwi)
Implement support for labeled MRM experiments, Q1 m/z value and charges. (Andreas)
Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)
test performance and make fitGumbelGauss available via parameters.
allow charge state based fitting
allow semi-supervised by using decoy annotations
allow non-parametric via kernel density estimation
ProteinInference -- Protein inference based on an aggregation of the scores of the identified peptides. Full documentation: http://www.openms.de/documentation/TOPP_ProteinInference.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 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: ProteinInference <options> Options (mandatory options marked with '*'): -in <file>* Input file(s) (valid formats: 'idXML') -out <file>* Output file (valid formats: 'idXML') -merge_runs <choice> If your idXML contains multiple runs, merge them beforehand? (default: 'no' valid: 'no', 'all') -annotate_indist_groups <choice> If you want to annotate indistinguishable protein groups, either for reporting or for group based quant. later. Only works with a single ID run in the file. (default: 'true' valid: 'true', 'false' ) Merging: -Merging:annotate_origin <choice> If true, adds a map_index MetaValue to the Peptid eIDs to annotate the IDRun they came from. (defau lt: 'true' valid: 'true', 'false') Algorithm: -Algorithm:min_peptides_per_protein <number> Minimal number of peptides needed for a protein identification. If set to zero, unmatched protein s get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evid ences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept. (default: '1' min: '0') -Algorithm:score_aggregation_method <choice> How to aggregate scores of peptides matching to the same protein? (default: 'maximum' valid: 'max imum', 'product', 'sum') -Algorithm:treat_charge_variants_separately <text> If this is set, different charge variants of the same peptide sequence count as individual evidenc es. (default: 'true') -Algorithm:treat_modification_variants_separately <text> If this is set, different modification variants of the same peptide sequence count as individual evidences. (default: 'true') -Algorithm:use_shared_peptides <text> If this is set, shared peptides are used as evide nces. (default: 'true') -Algorithm:skip_count_annotation <text> If this is true, peptide counts won't be annotate d at the proteins. (default: 'false') 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)INI file documentation of this tool:
Document which metavalues of Protein/PeptideHit are filled when reading ProtXML (Chris)
Writing of protXML is currently not supported
Handle Modifications (Andreas)
Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)