Percolator protocols

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Percolator statistics

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Percolator specifications

Information


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: https://github.com/percolator/percolator; https://bitbucket.org/jthalloran/percolator_upgrade/overview

Publications for Percolator

Percolator in pipelines

 (22)
2018
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 […]

2018
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 algorithm, and peptide areas were calculated using the precursor ions area detector node., identification and label-free quantification of ubiquitinated peptides in hela cells […]

2018
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 [] 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 […]

2018
PMCID: 5916898
PMID: 29695722
DOI: 10.1038/s41467-018-04084-0

[…] 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 […]

2017
PMCID: 5245905
PMID: 28060952
DOI: 10.1371/journal.ppat.1006145

[…] of cysteines and lysines. 10 ppm and 20 mda were used as mass accuracy for precursors and fragment ions, respectively. matched peptides were filtered using 1% false discovery rate calculated by percolator [] and in addition requiring that a peptide was matched as rank 1 and that precursor mass accuracy was better than 5 ppm. data from the co-immunoprecipitation experiment, in biological […]


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Percolator in publications

 (81)
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 […]

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 […]

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 […]

PMCID: 5825866
PMID: 29217756
DOI: 10.1242/dev.155838

[…] identified by mascot were further validated by manual inspection of the ms/ms spectra for the peptide to ensure the b- and y-ion series are sufficiently extensive for an accurate identification. percolator-based decoy searches () were also performed on the samples, and these revealed false discovery rates of 0%., micro-lenses were fixed for 1 h at room temperature in 2.5% glutaraldehyde […]

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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