Package: MSnID 1.39.0
Vlad Petyuk
MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.
Authors:
MSnID_1.39.0.tar.gz
MSnID_1.39.0.zip(r-4.5)MSnID_1.39.0.zip(r-4.4)MSnID_1.39.0.zip(r-4.3)
MSnID_1.39.0.tgz(r-4.4-any)MSnID_1.39.0.tgz(r-4.3-any)
MSnID_1.39.0.tar.gz(r-4.5-noble)MSnID_1.39.0.tar.gz(r-4.4-noble)
MSnID_1.39.0.tgz(r-4.4-emscripten)MSnID_1.39.0.tgz(r-4.3-emscripten)
MSnID.pdf |MSnID.html✨
MSnID/json (API)
NEWS
| # Install 'MSnID' in R: |
| install.packages('MSnID', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- msnidObj - Example mzIdenML File and MSnID Object
On BioConductor:MSnID-1.39.0(bioc 3.20)MSnID-1.38.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:2286916e5a
Exports:accessionsadd_mod_symbolapply_filterassess_missed_cleavagesassess_terminicorrect_peak_selectionevaluate_filterfetch_conversion_tableid_qualityinfer_parsimonious_accessionsmap_mod_sitesmass_measurement_errorMSnIDMSnIDFilteroptimize_filterpeptidesproteinspsmspsms<-read_mzIDsrecalibrateremap_accessionsremap_fasta_entry_namesreport_modsshowupdate
Dependencies:abindaffyaffyioAnnotationDbiAnnotationFilterAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocStyleBiocVersionBiostringsbitbit64bitopsblobbookdownbslibcachemcaToolscliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdoParalleldplyredgeRevaluatefansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsmsmsEDAmsmsTestsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplogrplotlyplyrpngpreprocessCorepromisesProtGenericsPSMatchpurrrQFeaturesqvalueR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownRSQLiteRUnitS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| MSnID: Utilities for Handling MS/MS Identifications | MSnID-package |
| Non-redundant list of accession (protein) identifiers | accessions proteins |
| Annotates peptide sequences with modification symbols | add_mod_symbol add_mod_symbol,MSnID-method |
| Filters the MS/MS identifications | apply_filter apply_filter,MSnID,character-method apply_filter,MSnID,MSnIDFilter-method |
| Counts the missing cleavage sites within the peptides sequence | assess_missed_cleavages |
| Checks if the peptide termini conforms with cleavage specificity | assess_termini |
| Corrects wrong selection of monoisotopic peak | correct_peak_selection |
| Filters the MS/MS identifications | evaluate_filter |
| Fetches conversion table form one type of identifiers to another | fetch_conversion_table |
| Identification quality | id_quality |
| Eliminates Redundancy in Peptide-to-Protein Mapping | infer_parsimonious_accessions infer_parsimonious_accessions,MSnID-method |
| Maps the modifications to protein sequence | map_mod_sites map_mod_sites,MSnID-method |
| Computes error of the parent ion mass to charge measurement | mass_measurement_error |
| The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data | $,MSnID-method $<-,MSnID-method accessions,MSnID-method assess_missed_cleavages,MSnID-method assess_termini,MSnID-method class:MSnID coerce,MSnID,data.table-method coerce,MSnID,MSnSet-method correct_peak_selection,MSnID-method dim,MSnID-method evaluate_filter,MSnID-method id_quality,MSnID-method mass_measurement_error,MSnID-method MSnID MSnID-class names,MSnID-method peptides,MSnID-method proteins,MSnID-method psms,MSnID-method psms<-,MSnID,data.frame-method read_mzIDs,MSnID-method recalibrate,MSnID-method show,MSnID-method [[,MSnID,ANY,ANY-method [[,MSnID-method [[<-,MSnID,ANY,ANY,ANY-method |
| The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. | $,MSnIDFilter-method $<-,MSnIDFilter-method as.numeric,MSnIDFilter-method class:MSnIDFilter length,MSnIDFilter-method MSnIDFilter MSnIDFilter-class names,MSnIDFilter-method show,MSnIDFilter-method update,MSnIDFilter-method |
| Example mzIdenML File and MSnID Object | c_elegans msnidObj |
| Filter criteria optimization to maximize the number of identifications given the FDR upper threshold | optimize_filter optimize_filter,MSnIDFilter,MSnID-method |
| Non-redundant list of peptides | peptides |
| Peptide-to-spectrum matches | psms psms<- |
| Populates MS/MS results table from mzIdentML files | read_mzIDs |
| Post-experimental recalibration of observed mass to charge ratios | recalibrate |
| Changes accessions from one protein id to another | remap_accessions remap_accessions,MSnID-method |
| Remapping entries in FASTA file | remap_fasta_entry_names |
| Lists modification masses in the MSnID object | report_mods report_mods,MSnID-method |
