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Parsing pepXML files and filter based on peptide FDR.

Bioconductor version: Release (3.19)

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

Author: Xiaojing Wang

Maintainer: Xiaojing Wang < at>

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


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:

Introduction to pepXMLTab PDF R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends R (>= 3.0.1)
Imports XML (>= 3.98-1.1)
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Suggests RUnit, BiocGenerics
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Follow Installation instructions to use this package in your R session.

Source Package pepXMLTab_1.38.0.tar.gz
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macOS Binary (x86_64) pepXMLTab_1.38.0.tgz
macOS Binary (arm64) pepXMLTab_1.38.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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