IDPicker protocols

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IDPicker specifications

Information


Unique identifier OMICS_05381
Name IDPicker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License Apache License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Publications for IDPicker

IDPicker in pipelines

 (9)
2018
PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17

[…] the sequenced genome of desulfobulbus oralis, concatenated with common contaminants and reversed-decoy sequences using myrimatch version 2.2 (). peptides were identified and proteins inferred using idpicker version 3.1 () with an experimental false-discovery rate (fdr) of <1% at the peptide level. peptide abundances were derived in idpicker by extracting precursor intensities/area […]

2017
PMCID: 5327387
PMID: 28240279
DOI: 10.1038/srep43583

[…] 27405 proteome database – concatenated with common contaminants and reversed protein entries to assess false-discovery rates (fdr) – using myrimatch v. 2.1. peptide spectrum matches were filtered by idpicker v.3 (fdr < 1%), assigned matched-ion intensities, and peptide abundance distributions normalized and assembled to proteins using infernordn, as previously described. for statistical […]

2017
PMCID: 5468372
PMID: 28659875
DOI: 10.3389/fmicb.2017.01020

[…] match ms/ms spectra to peptide sequences (), including partial tryptic cleavage peptides, dynamic modification of methionine oxidations, and maximum 10 ppm parent ion mass tolerance in the search. idpicker 3.0 was used to filter peptide-spectrum matches to 2% fdr and apply parsimony filtering to derive a minimum protein list, with each protein supported by at least two distinct peptides (; ). […]

2016
PMCID: 4788478
PMID: 26989779
DOI: 10.1126/sciadv.1501254

[…] 1313 proteome database concatenated with common contaminants and reversed sequences to control false discovery rates using myrimatch v.2.1 (). peptide spectrum matches (psms) were filtered by idpicker v.3 () and assigned matched-ion intensities (mits) based on observed peptide fragment peaks. psm mits were summed on a per-peptide basis, and only those uniquely and specifically matching […]

2016
PMCID: 4890492
PMID: 27257435
DOI: 10.1186/s13068-016-0528-8

[…] 1313 proteome database concatenated with common contaminants and reversed sequences to control false-discovery rates using myrimatch v.2.1 []. peptide spectrum matches (psm) were filtered by idpicker v.3 [] using a peptide-level fdr of <1 % per sample run and assigned matched-ion intensities (mit) based on observed peptide fragment peaks. psm mits were summed on a per-peptide basis, […]


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IDPicker in publications

 (65)
PMCID: 5893878
PMID: 29636439
DOI: 10.1128/mBio.00441-18

[…] protein sequences, which were used to control the false-discovery rate (fdr). collected ms/ms spectra were matched to peptides using myrimatch v2.1 (), filtered, and assembled into proteins using idpicker v3.0 (). all searches included the following peptide modifications: a static cysteine modification (+57.02 da), an n-terminal dynamic carbamylation modification (+43.00 da), and a dynamic […]

PMCID: 5865380
PMID: 29588665
DOI: 10.1186/s13068-018-1076-1

[…] and decoy sequences using myrimatch v. 2.1 []. peptide spectral matches (psm) were filtered to achieve peptide false-discovery rates (fdr) < 1% and assembled to their respective proteins using idpicker v. 3.0 []. protein abundances were derived via peptide ion intensity values as previously described []. extracellular proteins were analyzed independently by computationally removing psort- […]

PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17

[…] the sequenced genome of desulfobulbus oralis, concatenated with common contaminants and reversed-decoy sequences using myrimatch version 2.2 (). peptides were identified and proteins inferred using idpicker version 3.1 () with an experimental false-discovery rate (fdr) of <1% at the peptide level. peptide abundances were derived in idpicker by extracting precursor intensities/area […]

PMCID: 5813909
PMID: 29447168
DOI: 10.1371/journal.pone.0190019

[…] and a dynamic modification corresponding to an oxidation (+15.9949 da) of methionine. for protein inference and post-search filtering, database search results for each sample were merged together in idpicker v3.1.643 []. to achieve an experimental false discovery rate (fdr) of <1% at the peptide level, we enforced protein identifications to have at least two distinct peptide identifications […]

PMCID: 5836368
PMID: 29222161
DOI: 10.1074/mcp.RA117.000155

[…] y-ions as major fragments. thermo raw files are accessible through ftp://massive.ucsd.edu/msv000081188/updates/2017-10-19_xjwang_ad93f39b/raw/., for each data set generated using a specific enzyme, idpicker v3.0.564() was used to report the peptide identifications that coupled together 15 files searched by ms-gf+ beta (v9517) () and myrimatch v2.1.132() against refseq human protein database […]


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IDPicker institution(s)
Department of Biomedical Informatics, Mass Spectrometry Research Center; Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN

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