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OpenMS
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PercolatorAdapter facilitates the input to, the call of and output integration of Percolator. Percolator (http://percolator.ms/) is a tool to apply semi-supervised learning for peptide identification from shotgun proteomics datasets.
pot. predecessor tools | → PercolatorAdapter → | pot. successor tools |
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PSMFeatureExtractor | IDFilter |
Percolator is search engine sensitive, i.e. it's input features vary, depending on the search engine. Must be prepared beforehand. If you do not want to use the specific features, use the generic_feature_set flag. Will incorporate the score attribute of a PSM, so be sure, the score you want is set as main score with IDScoreSwitcher . Be aware, that you might very well experience a performance loss compared to the search engine specific features. You can also perform protein inference with percolator when you activate the protein fdr parameter. Additionally you need to set the enzyme setting. We only read the q-value for protein groups since Percolator has a more elaborate FDR estimation. For proteins we add q-value as main score and PEP as metavalue. For PSMs you can choose the main score. Peptide level FDRs cannot be parsed and used yet.
Multithreading: The thread parameter is passed to percolator. Note: By default, a minimum of 3 threads is used (default of percolator) even if the number of threads is set to e.g. 1 for backwards compatibility reasons. You can still force the usage of less than 3 threads by setting the force flag.
The command line parameters of this tool are:
INI file documentation of this tool:
Percolator is written by Lukas Käll (http://per-colator.com/ Copyright Lukas Käll lukas.nosp@m..kal.nosp@m.l@sci.nosp@m.life.nosp@m.lab.s.nosp@m.e)