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specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: Release (3.19)

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>

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


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:

Automatic specL Workflow HTML R Script
Introduction to specL HTML R Script
Reference Manual PDF


biocViews MassSpectrometry, Proteomics, Software
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3)
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Suggests BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4)
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Suggests Me msqc1, NestLink
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Follow Installation instructions to use this package in your R session.

Source Package specL_1.38.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) specL_1.38.0.tgz
macOS Binary (arm64) specL_1.38.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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