Introduction | Workflow | Prologue - How to get the input for the specL package? | Read from redundant plus non-redundant blib files | Read from Mascot result files | Annotate protein IDs using FASTA | Generate the spectral library (assay) | Normalizing the retention time using iRT peptides | Generate the spectral library having no iRTs | Write output to file | Epilogue | What can I do with that library now? | Benchmark | Acknowledgement | TODO for next releases | Session information | References
Package: specL 1.47.0
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:
specL_1.47.0.tar.gz
specL_1.47.0.zip(r-4.7)specL_1.47.0.zip(r-4.6)specL_1.47.0.zip(r-4.5)
specL_1.47.0.tgz(r-4.6-any)specL_1.47.0.tgz(r-4.5-any)
specL_1.47.0.tar.gz(r-4.7-any)specL_1.47.0.tar.gz(r-4.6-any)
specL_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
specL/json (API)
| # 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:
- iRTpeptides - IRT peptides - independent retention time peptides
- ms1.p2069 - Ms1 mass
- peptideStd - Peptide standard
- peptideStd.redundant - Peptide standard
On BioConductor:specL-1.47.0(bioc 3.24)specL-1.46.0(bioc 3.23)
massspectrometryproteomicsddadiamass-spectrometry
Last updated from:e53853a540. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 161 | ||
| linux-devel-x86_64 | NOTE | 247 | ||
| source / vignettes | OK | 193 | ||
| linux-release-x86_64 | NOTE | 189 | ||
| macos-release-arm64 | NOTE | 94 | ||
| macos-oldrel-arm64 | NOTE | 112 | ||
| windows-devel | NOTE | 93 | ||
| windows-release | NOTE | 92 | ||
| windows-oldrel | NOTE | 86 | ||
| wasm-release | OK | 109 |
Exports:annotate.protein_idcdswgenerate.consensusgenSwathIonLibgetProteinPeptideTableionlibrarymerge.specLSetplotplot.psmplot.psmSetread.bibliospecrt.inputrt.normalizedshowsummarysummary.psmSetwrite.spectronaut
Dependencies:ade4bitbit64blobcachemclicpp11DBIfastmapgluelatticelifecycleMASSmemoisenlmepixmappkgconfigprotVizRcppRcppArmadillorlangRSQLitesegmentedseqinrspvctrs
Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Last update: 2022-12-08
Started: 2022-12-07
specL automatic report
Requirements | Input | Parameter | Define the fragment ions of interest | Read the sqlite files | Protein (re)-annotation | Peptides used for RT normalization | Generate the ion library | Library Generation Summary | Output | Remarks | Session info | References
Last update: 2022-12-07
Started: 2017-04-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate protein_id | annotate.protein_id |
| Generate Dynamic SWATH Window | cdsw generateDynamicSwathWindow |
| Spectrum library generator for SWATH analysis | genSwathIonLib MRM specL SWATH swath |
| iRT peptides - independent retention time peptides | iRT irt iRTpeptides |
| ms1 mass | ms1.p2069 |
| Peptide standard | peptideStd peptideStd.redundant |
| Method for Function 'plot' in Package 'specL' | plot,ANY-method plot,specL-methods plot,specLSet-methods plot-methods |
| BiblioSpec Reader | BiblioSpec 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 |
