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This is the development version of MSnID; for the stable release version, see MSnID.

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

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Handling Modifications with MSnID PDF R Script
MSnID Package for Handling MS/MS Identifications PDF R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.39.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License Artistic-2.0
Depends R (>= 2.10), Rcpp
Imports MSnbase(>= 1.12.1), mzID(>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable
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Follow Installation instructions to use this package in your R session.

Source Package MSnID_1.39.0.tar.gz
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macOS Binary (x86_64) MSnID_1.39.0.tgz
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Source Repository (Developer Access) git clone
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