PeptideProphet protocols

PeptideProphet specifications


Unique identifier OMICS_02520
Name PeptideProphet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for PeptideProphet

PeptideProphet IN pipelines

PMCID: 5427775
PMID: 28579927
DOI: 10.2174/1570164614666161228124801

[…] against the ncbi rat protein database using the sequest algorithm (thermo electron, san jose, ca). the resulting sequest output files were loaded for identification of peptides and proteins using peptideprophet and proteinprophet software [15, 16], and assembled a complete protein list from the rat urine fractions using the interact software [17]. in addition, the peptide identification […]

PMCID: 5508000
PMID: 28751888
DOI: 10.3389/fmicb.2017.01328

[…] on cysteine (+71.037109 da) were set as variable modifications. protein identification results were evaluated by determination of probability for peptide and protein assignments provided by peptideprophet and proteinprophet (isi seattle, wa, united states) incorporated in the scaffold software package rel. 4.3.2 (proteome software, portland, or, united states). proteins were identified […]

PMCID: 5518268
PMID: 28744480
DOI: 10.1128/mSphere.00207-17

[…] [nq]). database search results were curated in scaffold (proteome software) to a 0.38% peptide false-discovery rate (fdr) and 0.5% protein fdr, using decoy database searching and the peptideprophet algorithm., rna was collected from 3 wells of a 6-well plate of infected cells at 16 hpi using an rneasy plus minikit (qiagen; catalog no. 74134). a2en, hela-cas9, and hela-cas9 ko […]

PMCID: 5620248
PMID: 28978108
DOI: 10.18632/oncotarget.19277

[…] database (version oct 5, 2010; 20,259 reviewed sequences; 75,498 non-reviewed sequences) using sorcerer™-sequest® (sage-n research). the quality of peptide and protein assignments was assessed using peptideprophet and proteinprophet. proteins with probabilities of ≥ 1.0 and ≥ 2 unique peptides were accepted as confidently identified peptides., to delineate the role of candidate genes […]

PMCID: 4727420
PMID: 26673204
DOI: 10.1194/jlr.M063701

[…] the mass tolerance for precursor ions was 2.5 ppm; sequest default tolerance was 2.5 da for precursor ion mass and 1 da for fragment ion mass. sequest results were further validated with peptideprophet and proteinprophet (22, 23), using an adjusted probability of ≥0.90 for peptides and ≥0.95 for proteins. each charge state of a peptide was considered a unique identification., we used […]

PeptideProphet institution(s)
Institute for Systems Biology, Seattle, WA, USA

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