PeptideProphet protocols

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PeptideProphet specifications

Information


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

 (73)
2018
PMCID: 5775567
PMID: 29351798
DOI: 10.1186/s12967-018-1388-8

[…] (+ 57.021 da), variable modification gln ⟶ pyro-glu of the n-terminus, oxidation of methionine (+ 15.995 da), and itraq 8-plex modification of lysine and peptide n termini (+ 304.205 da). we used peptideprophet and proteinprophet probabilities ≥ 0.95 to ensure an overall false discovery rate (fdr) below 1% and at least 1 unique peptide was qualified for further quantitative analysis. the fold […]

2018
PMCID: 5916935
PMID: 29695737
DOI: 10.1038/s41598-018-24270-w

[…] 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. […]

2018
PMCID: 5931751
PMID: 29732401
DOI: 10.1126/sciadv.aao1478

[…] 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., a hupb deletion strain was constructed using previously published protocols to make unmarked deletion mutants […]

2017
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 [, ], and assembled a complete protein list from the rat urine fractions using the interact software []. in addition, the peptide identification processes […]

2017
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 […]


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PeptideProphet in publications

 (325)
PMCID: 5941328
PMID: 29739327
DOI: 10.1186/s12870-018-1304-7

[…] mzxml data was then matched with the swiss-prot/trembl database (release-2015_07) (http://www.uniprot.org/uniprot) [, ] using the peptideprophet tool in trans-proteomic pipeline software (http://www.proteomecenter.org) []. the matching results were obtain using pepxmltab software. the following search parameter settings […]

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

[…] 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., a hupb deletion strain was constructed using previously published protocols to make unmarked deletion mutants […]

PMCID: 5916935
PMID: 29695737
DOI: 10.1038/s41598-018-24270-w

[…] 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. […]

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

[…] 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 […]

PMCID: 5897750
PMID: 29682498
DOI: 10.3389/fchem.2018.00095

[…] scan., peptides were matched with wine proteins by using the mascot software (www.matrixscience.com) within the ncbi, tandem and comet databases. validation of proteins was carried via protein and peptideprophet (tools.proteomecenter.org/tpp.php). peptides were filtered in order to keep peptides that were found in two of the three technical replicates for one white wine sample. peptides […]


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

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