ProteinProphet protocols

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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Publication for ProteinProphet

ProteinProphet IN pipelines

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 [15, 16], and assembled a complete protein list from the rat urine fractions using the interact software [17]. in addition, the peptide identification processes […]

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 […]

PMCID: 5620248
PMID: 28978108
DOI: 10.18632/oncotarget.19277

[…] 5, 2010; 20,259 reviewed sequences; 75,498 non-reviewed sequences) using sorcerer™-sequest® (sage-n research). the quality of peptide and protein assignments was assessed using peptideprophet and proteinprophet. proteins with probabilities of ≥ 1.0 and ≥ 2 unique peptides were accepted as confidently identified peptides., to delineate the role of candidate genes in the apoptotic process […]

PMCID: 5755722
PMID: 29321818
DOI: 10.18632/genesandcancer.159

[…] human protein database using x! tandem. the x! tandem search results were analyzed by the trans- proteomic pipeline [33] version 4.3. peptide/protein identifications were validated by peptide/proteinprophet [34, 35]., de-identified ewing sarcoma tumor rna samples and normal tonsil rna samples were obtained from the cooperative human tissue network. total cellular rna was isolated using […]

PMCID: 4727420
PMID: 26673204
DOI: 10.1194/jlr.M063701

[…] tolerance for precursor ions was 2.5 ppm; sequest default tolerance was 2.5 da for precursor ion mass and 1 da for fragment ion mass. sequest results were further validated with peptideprophet and proteinprophet (22, 23), using an adjusted probability of ≥0.90 for peptides and ≥0.95 for proteins. each charge state of a peptide was considered a unique identification., we used the gene […]

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

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