PeptideProphet pipeline

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 citations

 (15)
2017
PMCID: 5641917

[…] beavis, 2004), to increase both the number of protein identifications and the confidence in the data obtained. on this platform, peptide identifications from each search engine are validated with peptideprophet (nesvizhskii et al, 2003; keller et al, 2005). to increase the confidence in the data obtained, results were set at the 1% false discovery rate (elias & gygi, 2007)., normalized […]

2017
PMCID: 5620248

[…] database (version oct 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 […]

2015
PMCID: 4632068

[…] using the following variable modifications: silac heavy arginine: 13c6-15n4 (mw = 10.01), and silac heavy lysine: 13c6-15n2 (mw = 8.01). after assessment of peptide and protein identifications by peptideprophet (keller et al. 2002) and proteinprophet (nesvizhskii et al. 2003), quantitative silac ratios for proteins were determined using xpress software (han et al. 2001). precursor ion elution […]

2014
PMCID: 3938046

[…] and, +2.99826 da on asn residues for 18o-deamidation. for analysis of the n-glycoproteome, the database search output results were validated using trans-proteome pipeline (tpp), version 4.5 with the peptideprophet and proteinprophet algorithms [30]., the ms data from the ltq orbitrap velos were processed in maxquant, version 1.2.2.5 [31] using the andromeda search engine [32]. precursor ms […]

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

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