ProteinProphet pipeline

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 citations

PMCID: 4851412

[…] labeling if a component peptide displaying the addition of the biotin tag was identified from at least one high-quality spectrum in the same biological replicate in which the protein was inferred by proteinprophet. for each set of psms generated from the comet or the x!tandem search of the data from a given biological replicate, the prevalence of psms matching decoys among the putatively-labeled […]

PMCID: 3686733

[…] protein sequence database. the average fdr for 19 2d-lc-ms/ms experiments was 1.3%. following file conversion into the mzxml format, ms data were re-scored using the algorithms peptideprophet™ and proteinprophet™ [28], [29]. prot.xml files were analysed using an in house-developed software tool termed apex quantitative proteomics tool v1.1 [30]. using a pre-defined set of ms analysis […]

PMCID: 3633374

[…] was further processed using scaffold q + s (version 3.6.1, proteome software). upon import, the data were searched using x!tandem (the global proteome machine organization). peptideprophet and proteinprophet (institute for systems biology) probability thresholds of 95% were calculated from the decoy searches and scaffold was used to calculate an improved 95% peptide and protein probability […]

PMCID: 3365017

[…] zero to eliminate sample loading bias. protein inference was performed using proteinprophet [107]. since only high-quality peptide identifications were used for protein inference, only proteins with proteinprophet probability <0.05 were rejected outright. protein identifications were further restricted to proteins for which at least two unique peptide sequences were identified. protein […]

PMCID: 2996310

[…] march-viii, ratios between heavy and light peptide peaks were determined using the asapratio algorithm [32]. ratios of individual peptides belonging to the same protein were grouped together using proteinprophet to obtain a ratio for the expression of each identified protein [32]. hffs express three known substrates of march-viii: transferrin receptor (tfr), mhc class i, and activated […]

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

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