iProphet specifications


Unique identifier OMICS_19549
Name iProphet
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Alexey Nesvizhskii <>

iProphet article

iProphet citations

PMCID: 5006368

[…] asparagine/glutamine and oxidized methionine were selected as variable modifications., the results from each search engine were analyzed through tpp (the trans-proteomic pipeline, v4.7) [95] via the iprophet pipeline [96]. saintexpress version 3.3 [97] was used with default parameters to calculate statistical significance of each potential protein–protein interaction relative to control samples. […]

PMCID: 3675828

[…] of peptides identifiable from the acquired fragment ion spectra, we searched the data sequentially with the search engines mascot (31), x!tandem (32), and omssa (23) and combined the results using iprophet (34). the generated list of peptide identifications was used to determine the probability value that matches 1% fdr threshold. all peptides matching this cutoff were then used to assemble […]

iProphet institution(s)
Institute for Systems Biology, Seattle, WA, USA; Department of Chemical and Biomolecular Engineering, the Hong Kong University of Science and Technology, Hong Kong; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Sciences, University of Zurich, Zurich, Switzerland; Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
iProphet funding source(s)
Supported in part by the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract No. N01-HV-28179, by NIH Grants R01 CA126239, R01 GM094231, R01 GM087221, by PM50 GMO76547/Center for Systems Biology, by NSF MRI No. 0923536, and the Systems Biology Initiative of the Duchy of Luxembourg.

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