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Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications.

Bioconductor version: 3.1

Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

Author: Vlad Petyuk with contributions from Laurent Gatto

Maintainer: Vlad Petyuk <petyuk at>

Citation (from within R, enter citation("MSnID")):


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PDF R Script MSnID Package for Handling MS/MS Identifications
PDF   Reference Manual
Text   NEWS


biocViews MassSpectrometry, Proteomics, Software
Version 1.2.0
In Bioconductor since BioC 3.0 (R-3.1) (1 year)
License Artistic-2.0
Depends R (>= 2.10), Rcpp
Imports MSnbase(>= 1.12.1), mzID(>= 1.3.5), R.cache, foreach, doParallel, parallel, reshape2, methods, iterators, data.table, Biobase, ProtGenerics
Suggests BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
Depends On Me
Imports Me
Suggests Me RforProteomics
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