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Repository proteomiqon_psmstatistics
Owner: galaxyp
Synopsis: The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.
To measure the similarity of in silico generated spectra and measured MS/MS scans we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem.
Additionally, we also record quality control parameters such as the mass difference between the precursor ion and the theoretically calulated mass or the uniquness of each score
in comparison to 'competing' peptides within the search space. The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned
quality scores into one single consensus score. Since the search space is extended by so called decoys - reversed counterparts of peptides within the search space - we can estimate the distribution
of 'true negatives' and calculate local (PEP values) and global (Q values) false discovery rates at each consensus score. The reported peptides at user defined local and global FDR cutoffs can then
be used as inputs for any downstream analysis be it ProteinInference or PSMBasedQuantification.
Type: unrestricted
Revision: 2:9ac2e8232c5c
This revision can be installed: True
Times cloned / installed: 146

Contents of this repository

Name Description Version Minimum Galaxy Version
utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. 0.0.8 20.05

Categories
Proteomics - Tools enabling the study of proteins