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Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: Release (3.19)

The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

Author: Laurent Gatto, Nick J. Bond, Pavel V. Shliaha and Sebastian Gibb.

Maintainer: Laurent Gatto <laurent.gatto at> Sebastian Gibb <mail at>

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


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:

Combining HDMSe/MSe data using 'synapter' to optimise identification and quantitation HTML R Script
Fragment matching using 'synapter' HTML R Script
Synapter2 and synergise2 HTML R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.28.0
In Bioconductor since BioC 2.11 (R-2.15) (12 years)
License GPL-2
Depends R (>= 3.1.0), methods, MSnbase(>= 2.1.2)
Imports RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, Biostrings, cleaver(>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0)
System Requirements
See More
Suggests synapterdata(>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr
Linking To
Depends On Me synapterdata
Imports Me
Suggests Me
Links To Me
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Package Archives

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

Source Package synapter_2.28.0.tar.gz
Windows Binary
macOS Binary (x86_64) synapter_2.28.0.tgz
macOS Binary (arm64) synapter_2.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive