Percolator specifications


Unique identifier OMICS_02523
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



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Additional information

Percolator is available on Github and Bitbucket:;

Percolator articles

Percolator citations

PMCID: 5916898

[…] into proteins, and isobaric label quantification were performed using proteome discoverer 2.1 (thermo). we used the built-in processing workflow “pwf_fusion_reporter_based_quan_sps_ms3_sequestht_percolator” and the built-in consensus workflow “cwf_comprehensive_enhanced annotation_quan_results,” both with default settings. we used the tmt 10-plex quantification method with the 131 mass set […]

PMCID: 5885379

[…] variable modification of oxidized methionine, and static modifications for tmt reagents (peptide n-term and lysines) and alkylated cysteines. peptide sequence assignments were validated using percolator [33] q-values (less than 0.05) and 20 ppm delta mass agreement between measured and theoretical peptide masses. tmt reporter ion intensities of individual peptides were exported as text […]

PMCID: 5797217

[…] peptides. the peptide mass tolerance was set to ± 5 ppm and the fragment mass tolerance to ± 30 mmu. the maximal number of missed cleavages was set to 2. the result was filtered to 1% fdr using percolator algorithm integrated in proteome discoverer. the localization of the phosphorylation sites within the peptides was performed with the tool phosphors61., for the mapping of ub sites shown […]

PMCID: 5797244

[…] were allowed. static modification was set as cysteine carboxyamidation and dynamic modification was set as methionine oxidation. false discovery rates (fdr) were automatically calculated by the percolator node of pd based on decoy database hits. a peptide fdr of 0.01 were used for cut-offs. peptides with high confidence were considered as true hits and proteins with at least two different […]

PMCID: 5712195

[…] (+14.016 da; k, r), dimethyl (+28.031 da; k, r), trimethyl (+42.047 da; k, r), glygly (+114.043 da; k) and oxidation (+15.995 da; m, p) fixed modification: carbamidomethyl (+57.021 da; c). the percolator was used for the processing node and the cutoff limit false discovery rate (fdr) value was set to 0.01. the selected spectra were used for the identification of histone proteins […]

Percolator institution(s)
Department of Genome Sciences, University of Washington; William H Foege Building, Seattle, WA, USA

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