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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


No version available

Publication for PeptideProphet

PeptideProphet citations


Potential molecular mechanisms of overgrazing induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data

BMC Plant Biol
PMCID: 5941328
PMID: 29739327
DOI: 10.1186/s12870-018-1304-7
call_split See protocol

[…] mzXML data was then matched with the Swiss-Prot/TrEMBL database (release-2015_07) ( [, ] using the PeptideProphet tool in Trans-Proteomic Pipeline software ( []. The matching results were obtain using pepXMLTab software. The following search parameter settings were use […]


Posttranslational modification of a histone like protein regulates phenotypic resistance to isoniazid in mycobacteria

Sci Adv
PMCID: 5931751
PMID: 29732401
DOI: 10.1126/sciadv.aao1478

[…] ification, and oxidation on methionine, acetylation on lysine, and acetylation on protein N terminus were specified as variable modifications. Peptides were filtered at a 1% false discovery rate with PeptideProphet and grouped into proteins with ProteinProphet with a cutoff of 0.95. […]


Multi lectin Affinity Chromatography and Quantitative Proteomic Analysis Reveal Differential Glycoform Levels between Prostate Cancer and Benign Prostatic Hyperplasia Sera

Sci Rep
PMCID: 5916935
PMID: 29695737
DOI: 10.1038/s41598-018-24270-w
call_split See protocol

[…] e resulting mzXML files were used to identify proteins by searching against human UniProtKB database on the LabKey server using X!Tandem algorithm–. Search results from X!Tandem were then analyzed by PeptideProphet and validated using ProteinProphet,. Protein groups and peptides with a score greater than 0.9 and 0.6, respectively, were retained for protein identification and quantitation. Heavy-to […]


HATRIC based identification of receptors for orphan ligands

Nat Commun
PMCID: 5904110
PMID: 29666374
DOI: 10.1038/s41467-018-03936-z

[…] ecursor mass tolerance was set to 20 p.p.m. Carbamidomethylation was set as a fixed modification for cysteine and oxidation of methionine as a variable modification. Probability scoring was done with PeptideProphet and ProteinProphet of the Trans-Proteomic Pipeline (v4.6.2). Protein identifications were filtered for a FDR of ≤1%. For label-free quantification, proteins were filtered for cell surfa […]


Molecular and Macromolecular Changes in Bottle Aged White Wines Reflect Oxidative Evolution–Impact of Must Clarification and Bottle Closure

PMCID: 5897750
PMID: 29682498
DOI: 10.3389/fchem.2018.00095
call_split See protocol

[…] s MS scan.Peptides were matched with wine proteins by using the MASCOT software ( within the NCBI, Tandem and Comet databases. Validation of proteins was carried via Protein and PeptideProphet ( Peptides were filtered in order to keep peptides that were found in two of the three technical replicates for one white wine sample. Peptides retenti […]


Differential accumulation of proteins in oil palms affected by fatal yellowing disease

PLoS One
PMCID: 5886584
PMID: 29621343
DOI: 10.1371/journal.pone.0195538
call_split See protocol

[…] rsion 4.5.1, Proteome Software Inc., Portland, OR). Protein identification was only accepted if the peptide identification probability was greater than 90% and proteins greater 95% accordingly to the peptideprophet and proteinprophet algorithms []. Differentially expressed proteins were determined by applying a permutation test with significance level grater than 95% (p < 0.05). Statistical signif […]


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

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