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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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Versioning


No version available

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 citations

 (209)
call_split

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

2018
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. […]

call_split

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

2018
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 […]

call_split

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

2018
Oncotarget
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 […]

call_split

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

2018
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 […]

call_split

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

2018
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 […]

library_books

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

2018
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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