Percolator statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Percolator

Tool usage distribution map

This map represents all the scientific publications referring to Percolator per scientific context
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Associated diseases

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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


A subset of mobilized human hematopoietic stem cells express germ layer lineage genes which can be modulated by culture conditions

PMCID: 5930965
PMID: 29720239
DOI: 10.1186/s13287-018-0858-5
call_split See protocol

[…] ermo Scientific) using the Sequest HT search engine to match acquired spectra against a human subset of the Uniprot protein sequence database, which included sequences of common protein contaminants. Percolator was used to validate peptide-spectrum matches at a Q value [] (false discovery rate (FDR)) of 0.01. […]


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
call_split See protocol

[…] ions 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 as […]


PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia

PMCID: 5955148
PMID: 29774127
DOI: 10.18632/oncotarget.25204
call_split See protocol

[…] n of methionine, deamidation of asparagine and glutamine, phosphorylation of serine, threonine and tyrosine were considered as potential modifications. False discovery rate (FDR) was determined using Percolator and proteins/peptides with an FDR of ≤1% were retained for further analysis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partne […]


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

[…] avages, 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 files […]


Molecular characterization of ERBB2 amplified colorectal cancer identifies potential mechanisms of resistance to targeted therapies: a report of two instructive cases

PMCID: 5880263
PMID: 29438965
DOI: 10.1101/mcs.a002535
call_split See protocol

[…] ini were set as variable modifications. Carbamidomethylation of cysteine was set as a fixed modification. Peptide spectral match error rates were determined using the target-decoy strategy coupled to Percolator modeling of positive and false distributions (; ). Data were filtered at the peptide spectral match level to control for false discoveries using a q-value cutoff of 0.01 as determined by Pe […]


A Highly Efficient Xylan Utilization System in Aspergillus niger An76: A Functional Proteomics Study

Front Microbiol
PMCID: 5874446
PMID: 29623069
DOI: 10.3389/fmicb.2018.00430

[…] and carbamidomethyl of cysteine residues was selected as the fixed modification. Only peptides with at least six amino acid residues showing 95% certainty (q ≤ 0.05) were included in the results, the Percolator in Sequest HT was assigned to obtain Peptide Probabilities (Käll et al., ). At least one peptides (q < 0.05) was needed to be considered for protein identification and the false discovery r […]

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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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