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MSnID

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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MSnID")

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

Documentation

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

browseVignettes("MSnID")
Handling Modifications with MSnID PDF R Script
MSnID Package for Handling MS/MS Identifications PDF R Script
Reference Manual PDF
NEWS Text

Details

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
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Package Archives

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

Source Package MSnID_1.37.0.tar.gz
Windows Binary MSnID_1.37.0.zip
macOS Binary (x86_64) MSnID_1.37.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MSnID
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSnID
Bioc Package Browser https://code.bioconductor.org/browse/MSnID/
Package Short Url https://bioconductor.org/packages/MSnID/
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