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IDPicker specifications


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


No version available

Publications for IDPicker

IDPicker citations


Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

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

[…] rse 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 oxi […]


The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate

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

[…] inants 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- a […]


Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

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

[…] m 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 under the curv […]


Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves

PLoS One
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 and a […]


Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity*

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

[…] and y-ions as major fragments. Thermo RAW files are accessible through 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 vers […]


Maternal consumption of fish oil programs reduced adiposity in broiler chicks

Sci Rep
PMCID: 5640664
PMID: 29030616
DOI: 10.1038/s41598-017-13519-5

[…] d. MyriMatch v2.1.111 was used to search the raw mass spectra against the predicted protein database to identify fully-tryptic peptides, which were then grouped together into respective proteins with IDPicker v.3. Only protein identifications with at least two identified peptide spectra and a maximum q-value of 0.02 were considered for further analysis. Peptide fragments were mapped to proteins in […]


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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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