Package: specL 1.41.0

Christian Panse

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

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 <https://fgcz.ch>.

Authors:Christian Panse [aut, cre], Jonas Grossmann [aut], Christian Trachsel [aut], Witold E. Wolski [ctb]

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specL.pdf |specL.html✨
specL/json (API)
NEWS

# Install 'specL' in R:
install.packages('specL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fgcz/specl/issues

Datasets:

On BioConductor:specL-1.41.0(bioc 3.21)specL-1.40.0(bioc 3.20)

massspectrometryproteomicsddadiamass-spectrometry

5.46 score 1 stars 12 scripts 262 downloads 2 mentions 17 exports 27 dependencies

Last updated 4 months agofrom:bb4f519fe6. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
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Exports:annotate.protein_idcdswgenerate.consensusgenSwathIonLibgetProteinPeptideTableionlibrarymerge.specLSetplotplot.psmplot.psmSetread.bibliospecrt.inputrt.normalizedshowsummarysummary.psmSetwrite.spectronaut

Dependencies:ade4bitbit64blobcachemclicpp11DBIfastmapgluelatticelifecycleMASSmemoisenlmepixmappkgconfigplogrprotVizRcppRcppArmadillorlangRSQLitesegmentedseqinrspvctrs

specL automatic report

Christian Panse, Witold E. Wolski

Rendered fromreport.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2022-12-07
Started: 2017-04-14

Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Christian Panse, Christian Trachsel, Jonas Grossmann, Witold E. Wolski

Rendered fromspecL.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2022-12-08
Started: 2022-12-07

Readme and manuals

Help Manual

Help pageTopics
Annotate protein_idannotate.protein_id
Generate Dynamic SWATH Windowcdsw generateDynamicSwathWindow
Spectrum library generator for SWATH analysisgenSwathIonLib MRM specL SWATH swath
iRT peptides - independent retention time peptidesiRT irt iRTpeptides
ms1 massms1.p2069
Peptide standardpeptideStd peptideStd.redundant
Method for Function 'plot' in Package 'specL'plot,ANY-method plot,specL-methods plot,specLSet-methods plot-methods
BiblioSpec ReaderBiblioSpec bibliospec plot.psm plot.psmSet read.bibliospec Skyline skyline summary.psmSet
Methods for Function 'show' in Package 'specL' ~~show,ANY-method show-methods
Class '"specL"'plot,specL-method show,specL-method specL-class write.spectronaut,specL-method
Class '"specLSet"'generate.consensus generate.consensus,specLSet-method getProteinPeptideTable getProteinPeptideTable,specLSet-method ionlibrary ionlibrary,specLSet-method merge.specLSet merge.specLSet,specLSet-method plot plot,specLSet-method rt.input rt.input,specLSet-method rt.normalized rt.normalized,specLSet-method show,specLSet-method specLSet-class summary,specLSet-method write.spectronaut,specLSet-method
Methods for Function 'write.spectronaut' in Package 'specL'write.spectronaut write.spectronaut,ANY-method write.spectronaut,specL-methods write.spectronaut,specLSet-methods