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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


No version available

Publication for ProteinProphet

ProteinProphet citations


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

[…] ation 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

[…] o 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 fo […]


HATRIC based identification of receptors for orphan ligands

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

[…] nce 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

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

[…] me 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 (P-values) f […]


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

PLoS Negl Trop Dis
PMCID: 5897034
PMID: 29608573
DOI: 10.1371/journal.pntd.0006351

[…] arch 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) [] were […]


A Highly Efficient Xylan Utilization System in Aspergillus niger An76: A Functional Proteomics Study

Front Microbiol
PMCID: 5874446
PMID: 29623069
DOI: 10.3389/fmicb.2018.00430

[…] ate inference of protein abundance, this problem was solved by protein groups that involve shared peptides along with an Occam's razor constraint, and the solution method was embodied in the software ProteinProphet as reported by Nesvizhskii (Nesvizhskii et al., ). Significant difference (P < 0.05) was calculated by statistical analysis using t-test and one-way ANOVA methods in GraphPad prism 5.0 […]


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

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