iProphet protocols

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iProphet specifications


Unique identifier OMICS_19549
Name iProphet
Alternative name InterProphet
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 <>

Publication for iProphet

iProphet in pipeline

PMCID: 3675828
PMID: 23462206
DOI: 10.1074/mcp.M112.023754

[…] number of peptides identifiable from the acquired fragment ion spectra, we searched the data sequentially with the search engines mascot (), x!tandem (), and omssa () and combined the results using iprophet (). 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 […]

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iProphet in publications

PMCID: 5871760
PMID: 29593215
DOI: 10.1038/s41467-018-03387-6

[…] and analysis was carried out as described elsewhere. briefly, raw files were converted to.mzxml in proteowizard. peptide search and identification was processed using human refseq version 57 and the iprophet pipeline integrated in prohits., we used four different methods to identify wt aid–bioid interactions that were significantly and consistently reduced in both r-mutants tested. comparative […]

PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] files were searched with x! tandem and comet against the annotated yeast proteins database with included reversed decoy peptides. search results were scored using peptideprophet and combined with iprophet. mayu was used to estimate iprophet probabilities to control for protein identification false discovery rate (fdr <1%). the final spectral library was assembled using spectrast […]

PMCID: 5862596
PMID: 29568375
DOI: 10.18632/oncotarget.24418

[…] pipeline (tpp) v5.0 typhoon was used for protein identification as well as for quantitation. peptideprophet tool was used to assess the peptide spectral match (psm) for individual files whereas iprophet tool was used to combine individual peptideprophet files. further, proteinprophet was used for the identification of the proteins on the iprophet files and proteins with 1.0% fdr […]

PMCID: 5784136
PMID: 29367647
DOI: 10.1038/s41598-018-19931-9

[…] the search results from all four fractions and the lc/ms technical replicates were combined and further processed with the trans-proteomic pipeline (tpp) software suite, comprising peptideprophet, iprophet and proteinprophet. the protein false discovery rate (fdr) cut-off was set at 0.01. since the rabbit proteome is not well characterized, the functions of the uncharacterized rabbit proteins […]

PMCID: 5768655
PMID: 29375523
DOI: 10.3389/fmicb.2017.02658

[…] channel’s contribution by dividing the individual reporter ion intensities by the corresponding channel-specific correction factor. the pep.xml files obtained from peptideprophet were combined using iprophet () and the protein lists were assembled using proteinprophet (). the final protein ratios were calculated using libraproteinratioparser () and a concatenated target-decoy database-search […]

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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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