Registration and Call for Abstracts Open for Bioc2024


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 (3.19)

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.


Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
System Requirements
See More
Linking To
Depends On Me
Imports Me
Suggests Me RforProteomics
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats