DOI: 10.18129/B9.bioc.specL    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: 3.8

provides a function for generating spectra libraries which 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.

Author: Christian Trachsel [aut], Christian Panse [aut, cre] (0000-0003-1975-3064), Jonas Grossmann [aut] (0000-0002-6899-9020), Witold E. Wolski [ctb]

Maintainer: Christian Panse <cp at fgcz.ethz.ch>, Witold E. Wolski <wewolski at gmail.com>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



HTML R Script Automatic Workflow
HTML R Script Computing Dynamic SWATH Windows
PDF R Script Introduction to specL
HTML R Script Retention Time Prediction using the ssrc Method
PDF   Reference Manual
Text   NEWS


biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.16.1
In Bioconductor since BioC 3.0 (R-3.1) (4.5 years)
License GPL-3
Depends R (>= 3.3.2), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.2.45), RSQLite (>= 1.1.2), seqinr (>= 3.3.3)
Suggests BiocGenerics, BiocStyle(>= 2.2.1), knitr (>= 1.15.1), msqc1(>= 1.0.0), plotrix (>= 3.6.4), prozor (>= 0.2.2), RUnit (>= 0.4.31)
URL https://github.com/fgcz/specL
BugReports https://github.com/fgcz/specL/issues
Depends On Me
Imports Me
Suggests Me msqc1
Links To Me
Build Report  

Package Archives

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

Source Package specL_1.16.1.tar.gz
Windows Binary specL_1.16.1.zip
Mac OS X 10.11 (El Capitan) specL_1.16.1.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 http://bioconductor.org/packages/specL/
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