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ProteinProphet specifications


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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ProteinProphet citations


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

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 […]


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

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 […]


HATRIC based identification of receptors for orphan ligands

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 […]


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

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 […]


Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc STAMS2)

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) [] […]


Quantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas

PMCID: 5862596
PMID: 29568375
DOI: 10.18632/oncotarget.24418

[…] as for quantitation. peptideprophet tool was used to assess the peptide spectral match (psm) for individual files whereas iprophet tool was used to combine individual peptideprophet files. further, proteinprophet was used for the identification of the proteins on the iprophet files and proteins with 1.0% fdr were considered as a true identification for protein quantitation [–]. the quantitation […]

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

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