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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("specL")
AuthorChristian Trachsel [aut], Christian Panse [aut, cre], Jonas Grossmann [aut], Witold E. Wolski [ctb]
Bioconductor views MassSpectrometry Proteomics
Date of publicationNone
MaintainerChristian Panse <cp@fgcz.ethz.ch>, Witold E. Wolski <wewolski@gmail.com>
LicenseGPL-3
Version1.10.0
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

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R R/annotate.protein_id.R R/cdsw.R R/genSwathIonLib.R R/read.bibliospec.R R/specL.R R/specLSet.R R/ssrc.R R/zzz.R
README.md
build
build/vignette.rds
data
data/iRTpeptides.RData
data/ms1_p2069.RData
data/peptideStd.RData
inst
inst/CITATION
inst/Dockerfile
inst/NEWS.Rd
inst/doc
inst/doc/cdsw.R
inst/doc/cdsw.Rmd
inst/doc/cdsw.html
inst/doc/report.R
inst/doc/report.Rmd
inst/doc/report.html
inst/doc/specL.R
inst/doc/specL.Rnw
inst/doc/specL.pdf
inst/doc/ssrc.R
inst/doc/ssrc.Rmd
inst/doc/ssrc.html
inst/extdata
inst/extdata/SP201602-specL.fasta.gz
inst/extdata/peptideStd.sqlite
inst/extdata/peptideStd_redundant.sqlite
inst/unitTests
inst/unitTests/test_annotateProteinID.R inst/unitTests/test_cdsw.R inst/unitTests/test_genSwathIonLib.R inst/unitTests/test_merge.specLSet.R inst/unitTests/test_peptideStd.R inst/unitTests/test_read.bibliospec.R inst/unitTests/test_ssrc.R
man
man/annotate.protein_id.Rd man/cdsw.Rd man/genSwathIonLib.Rd man/iRTpeptides.Rd man/ms1.p2069.Rd man/peptideStd.Rd man/plot-methods.Rd man/read.bibliospec.Rd man/show-methods.Rd man/specL-class.Rd man/specLSet-class.Rd man/ssrc.Rd man/write.spectronaut-methods.Rd
src
src/Makevars
src/lower_bound.cpp
tests
tests/runTests.R
vignettes
vignettes/cdsw.Rmd
vignettes/ieee.csl
vignettes/ms1.p2069.Rdata
vignettes/report.Rmd
vignettes/specL.Rnw
vignettes/specL.bib
vignettes/ssrc.Rmd

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

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