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An mzIdentML parser for R

Bioconductor version: Release (3.19)

A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.

Author: Laurent Gatto [ctb, cre] , Thomas Pedersen [aut] , Vladislav Petyuk [ctb]

Maintainer: Laurent Gatto <laurent.gatto at>

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


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

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


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:

Using mzID PDF R Script
Reference Manual PDF


biocViews DataImport, ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.42.0
In Bioconductor since BioC 2.13 (R-3.0) (11 years)
License GPL (>= 2)
Depends methods
Imports XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics
System Requirements
See More
Suggests knitr, testthat
Linking To
Depends On Me
Imports Me MSnbase, MSnID, TargetDecoy
Suggests Me mzR, PSMatch, RforProteomics
Links To Me
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Package Archives

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

Source Package mzID_1.42.0.tar.gz
Windows Binary
macOS Binary (x86_64) mzID_1.42.0.tgz
macOS Binary (arm64) mzID_1.42.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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