specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

specL 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 <christian.trachsel@fgcz.uzh.ch>, Christian Panse <cp@fgcz.ethz.ch>, Jonas Grossmann <jg@fgcz.ethz.ch>, Witold E. Wolski <wewolski@gmail.com>
Date of publication
None
Maintainer
Christian Panse <cp@fgcz.ethz.ch>, Witold E. Wolski <wewolski@gmail.com>
License
GPL-3
Version
1.8.0
URLs

View on Bioconductor

Man pages

annotate.protein_id
Annotate protein_id
cdsw
Generate Dynamic SWATH Window
genSwathIonLib
Spectrum library generator for SWATH analysis
iRTpeptides
iRT peptides - independent retention time peptides
ms1.p2069
ms1 masses
peptideStd
Peptide standard
plot-methods
Method for Function 'plot' in Package 'specL'
read.bibliospec
BiblioSpec Reader
show-methods
Methods for Function 'show' in Package 'specL' ~~
specL-class
Class '"specL"'
specLSet-class
Class '"specLSet"'
ssrc
Sequence Specific Retention Calculator
write.spectronaut-methods
Methods for Function 'write.spectronaut' in Package 'specL'

Files in this package

specL/DESCRIPTION
specL/NAMESPACE
specL/R
specL/R/AllGenerics.R
specL/R/annotate.protein_id.R
specL/R/cdsw.R
specL/R/genSwathIonLib.R
specL/R/read.bibliospec.R
specL/R/specL.R
specL/R/specLSet.R
specL/R/ssrc.R
specL/R/zzz.R
specL/README.md
specL/build
specL/build/vignette.rds
specL/data
specL/data/iRTpeptides.RData
specL/data/ms1_p2069.RData
specL/data/peptideStd.RData
specL/inst
specL/inst/CITATION
specL/inst/Dockerfile
specL/inst/NEWS.Rd
specL/inst/doc
specL/inst/doc/cdsw.R
specL/inst/doc/cdsw.Rmd
specL/inst/doc/cdsw.html
specL/inst/doc/specL.R
specL/inst/doc/specL.Rnw
specL/inst/doc/specL.pdf
specL/inst/doc/ssrc.R
specL/inst/doc/ssrc.Rmd
specL/inst/doc/ssrc.html
specL/inst/extdata
specL/inst/extdata/peptideStd.sqlite
specL/inst/extdata/peptideStd_redundant.sqlite
specL/inst/unitTests
specL/inst/unitTests/test_annotateProteinID.R
specL/inst/unitTests/test_cdsw.R
specL/inst/unitTests/test_genSwathIonLib.R
specL/inst/unitTests/test_merge.specLSet.R
specL/inst/unitTests/test_peptideStd.R
specL/inst/unitTests/test_read.bibliospec.R
specL/inst/unitTests/test_ssrc.R
specL/man
specL/man/annotate.protein_id.Rd
specL/man/cdsw.Rd
specL/man/genSwathIonLib.Rd
specL/man/iRTpeptides.Rd
specL/man/ms1.p2069.Rd
specL/man/peptideStd.Rd
specL/man/plot-methods.Rd
specL/man/read.bibliospec.Rd
specL/man/show-methods.Rd
specL/man/specL-class.Rd
specL/man/specLSet-class.Rd
specL/man/ssrc.Rd
specL/man/write.spectronaut-methods.Rd
specL/src
specL/src/Makevars
specL/src/lower_bound.cpp
specL/tests
specL/tests/runTests.R
specL/vignettes
specL/vignettes/cdsw.Rmd
specL/vignettes/ieee.csl
specL/vignettes/ms1.p2069.Rdata
specL/vignettes/specL.Rnw
specL/vignettes/specL.bib
specL/vignettes/ssrc.Rmd