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.

AuthorChristian 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 publicationNone
MaintainerChristian Panse <cp@fgcz.ethz.ch>, Witold E. Wolski <wewolski@gmail.com>
LicenseGPL-3
Version1.8.0
https://github.com/fgcz/specL

View on Bioconductor

Functions

annotate.protein_id Man page
bibliospec Man page
BiblioSpec Man page
cdsw Man page
generate.consensus Man page
generate.consensus,specLSet-method Man page
generateDynamicSwathWindow Man page
genSwathIonLib Man page
getProteinPeptideTable Man page
getProteinPeptideTable,specLSet-method Man page
hydrophobicity Man page
ionlibrary Man page
ionlibrary Man page
ionlibrary,specLSet-method Man page
ionlibrary,specLSet-method Man page
irt Man page
iRT Man page
iRTpeptides Man page
merge.specLSet Man page
merge.specLSet,specLSet-method Man page
MRM Man page
ms1.p2069 Man page
peptideStd Man page
peptideStd.redundant Man page
plot Man page
plot,ANY-method Man page
plot-methods Man page
plot.psm Man page
plot.psmSet Man page
plot,specL-method Man page
plot,specL-methods Man page
plot,specLSet-method Man page
plot,specLSet-methods Man page
read.bibliospec Man page
rt.input Man page
rt.input,specLSet-method Man page
rt.normalized Man page
rt.normalized,specLSet-method Man page
show,ANY-method Man page
show-methods Man page
show,specL-method Man page
show,specLSet-method Man page
skyline Man page
Skyline Man page
specL Man page
specL-class Man page
specLSet-class Man page
ssrc Man page
summary.psmSet Man page
summary,specLSet-method Man page
swath Man page
SWATH Man page
write.spectronaut Man page
write.spectronaut,ANY-method Man page
write.spectronaut,specL-method Man page
write.spectronaut,specL-methods Man page
write.spectronaut,specLSet-method Man page
write.spectronaut,specLSet-methods Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.