Percolator pipeline

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



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Additional information

Percolator is available on Github and Bitbucket:;

Publications for Percolator

Percolator IN pipelines

PMCID: 5788924
PMID: 29379051
DOI: 10.1038/s41598-018-20130-9

[…] 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 algorithm55, and peptide areas were calculated using the precursor ions area detector node., identification and label-free quantification of ubiquitinated peptides in hela cells […]

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

[…] 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: 5481877
PMID: 28649280
DOI: 10.1186/s13068-017-0844-7

[…] of two missed cleavages allowed, carbamidomethylation of cysteines as a fixed modification and oxidation of methionine as a variable modification. peptides were validated through the algorithm percolator [23] and only those with high confidence were admitted (fdr 0.01). unless otherwise specified, protein identifications were accepted if they contained at least two identified peptides. […]

PMCID: 5579227
PMID: 28860535
DOI: 10.1038/s41598-017-09973-w

[…] arginines were selected as the variable modifications and carbamidomethylation at cysteines as the static modification. only peptides with a false discovery rate (fdr) below 0.01, as calculated by percolator61, and a peptide rank of one were considered as identified. the rank one peptide is the highest scoring match to a particular query and represents the most likely assignments. […]

PMCID: 5595437
PMID: 28898199
DOI: 10.7554/eLife.27480.049

[…] tmt6plex (k); variable modifications: oxidation (m), acetylation or tmt6plex (peptide n-terminus), met-loss (protein terminus). fdr was set to 1% by the target +decoy approach in conjunction with percolator (käll et al., 2007). reporter ions were extracted with an integration tolerance of 20 ppm. the resulting reporter ion abundance (s/n) was normalized using the total peptide approach […]

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

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