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Percolator specifications


Unique identifier OMICS_02523
Name Percolator
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




No version available

Additional information

Percolator is available on Github and Bitbucket:;

Publications for Percolator

Percolator citations


Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

Nat Commun
PMCID: 5916898
PMID: 29695722
DOI: 10.1038/s41467-018-04084-0

[…] we included the 6-plex tmt reagent mass (229.163 da) as a dynamic modification on lysine, histidine, serine, and threonine, as well as the peptide n terminus. fdr filtering was performed via percolator with a strict target fdr of 0.01 and a relaxed fdr of 0.05. strict parsimony was applied for protein grouping, and unique plus razor peptides were used for quantification. peptide […]


Coordinated responses to individual tumor antigens by IgG antibody and CD8+ T cells following cancer vaccination

PMCID: 5885379
PMID: 29618380
DOI: 10.1186/s40425-018-0331-0
call_split See protocol

[…] 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 [] 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 […]


Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores

Sci Rep
PMCID: 5788924
PMID: 29379051
DOI: 10.1038/s41598-018-20130-9
call_split See protocol

[…] acetylation and digly modification of lysine residues. cysteine carbamidomethylation was set as static modification. peptides were identified with a false discovery rate (fdr) of 1% estimated by percolator algorithm, and peptide areas were calculated using the precursor ions area detector node., identification and label-free quantification of ubiquitinated peptides in hela cells […]


SuperQuant assisted comparative proteome analysis of glioblastoma subpopulations allows for identification of potential novel therapeutic targets and cell markers

PMCID: 5823648
PMID: 29507698
DOI: 10.18632/oncotarget.24321

[…] spectra were processed with complementaryfinder node before database search. a detailed explanation of superquant data processing is published []. database search results were evaluated using percolator 2.05 [], with the standard feature set. all psms with q-value < 0.01 were grouped together using sequence and theoretical mass, and the highest percolator svm score was used […]


A reverse vaccinology approach to the identification and characterization of Ctenocephalides felis candidate protective antigens for the control of cat flea infestations

PMCID: 5774092
PMID: 29347954
DOI: 10.1186/s13071-018-2618-x

[…] discoverer 1.3; thermo scientific) with the constraints previously described []. for peptide validation, the proteome discoverer 1.3 software was used by filtering based on the q-value generated by percolator that is defined as the minimal false discovery rate (fdr) at with the identification is considered correct [, , ]. a fdr < 0.01 was considered as a condition for successful peptide […]


Biomechanical Rigidity and Quantitative Proteomics Analysis of Segmental Regions of the Trabecular Meshwork at Physiologic and Elevated Pressures

PMCID: 5770183
PMID: 29340639
DOI: 10.1167/iovs.17-22759

[…] monoisotopic masses, and trypsin cleavage (maximum two missed cleavages). searches used a reversed sequence decoy strategy to control peptide false discovery and identifications were validated by percolator software., search results and tmt reporter ion intensities were exported from proteome discoverer as text files and processed with in-house python scripts. only peptide spectrum matches […]

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

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