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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

Versioning


No version available

Publications for IDPicker

IDPicker citations

 (69)
library_books

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

2018
MBio
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 […]

library_books

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

2018
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 […]

call_split

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

2018
MBio
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 […]

library_books

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

2018
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 […]

call_split

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

2017
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 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 vers […]

library_books

Maternal consumption of fish oil programs reduced adiposity in broiler chicks

2017
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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