MSnID

DOI: 10.18129/B9.bioc.MSnID  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.32.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 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
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	MSnID_1.32.0.tar.gz
Windows Binary	MSnID_1.32.0.zip (64-bit only)
macOS Binary (x86_64)	MSnID_1.32.0.tgz
macOS Binary (arm64)	MSnID_1.32.0.tgz
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/
Package Downloads Report	Download Stats