DOI: 10.18129/B9.bioc.specL    

This is the development version of specL; for the stable release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: Development (3.15)

provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich .

Author: Christian Panse [aut, cre] , Jonas Grossmann [aut] , Christian Trachsel [aut], Witold E. Wolski [ctb]

Maintainer: Christian Panse <cp at fgcz.ethz.ch>

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


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

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

# The following initializes usage of Bioc devel


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:



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PDF R Script Introduction to specL
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biocViews MassSpectrometry, Proteomics, Software
Version 1.29.0
In Bioconductor since BioC 3.0 (R-3.1) (7 years)
License GPL-3
Depends R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.5), RSQLite (>= 1.1), seqinr (>= 3.3)
Suggests BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4)
URL http://bioconductor.org/packages/specL/
BugReports https://github.com/fgcz/specL/issues
Depends On Me
Imports Me
Suggests Me msqc1, NestLink
Links To Me
Build Report  

Package Archives

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

Source Package specL_1.29.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) specL_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/specL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/specL
Package Short Url https://bioconductor.org/packages/specL/
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