ProteinProphet protocols

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ProteinProphet specifications

Information


Unique identifier OMICS_02521
Name ProteinProphet
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 ProteinProphet

ProteinProphet in pipelines

 (72)
2018
PMCID: 5775567
PMID: 29351798
DOI: 10.1186/s12967-018-1388-8

[…] 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 changes in protein […]

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

[…] 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-light (h/l) ratioswere computed […]

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

[…] 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 by allelic exchange (). to generate […]

2017
PMCID: 5427775
PMID: 28579927
DOI: 10.2174/1570164614666161228124801

[…] 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

[…] (+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 by at least two […]


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ProteinProphet in publications

 (265)
PMCID: 5931751
PMID: 29732401
DOI: 10.1126/sciadv.aao1478

[…] 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 by allelic exchange (). to generate […]

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

[…] 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-light (h/l) ratioswere computed […]

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

[…] 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 surface location, based […]

PMCID: 5886584
PMID: 29621343
DOI: 10.1371/journal.pone.0195538

[…] 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 significance […]

PMCID: 5897034
PMID: 29608573
DOI: 10.1371/journal.pntd.0006351

[…] raw files converted to mzxml []. the mzxml files were searched by the comet search algorithm embedded into the tpp platform []. peptide and protein fdr was estimated using the peptideprophet and proteinprophet algorithm embedded in the trans-proteomic pipeline []. identifications with less than 1% fdr were kept., raw data from human placental tissue [] and t. vivax (meta, bsf1 and ep1) [] […]


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

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