Package: MSnID 1.41.0

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:Vlad Petyuk with contributions from Laurent Gatto

MSnID_1.41.0.tar.gz
MSnID_1.41.0.zip(r-4.5)MSnID_1.41.0.zip(r-4.4)MSnID_1.41.0.zip(r-4.3)
MSnID_1.41.0.tgz(r-4.4-any)MSnID_1.41.0.tgz(r-4.3-any)
MSnID_1.41.0.tar.gz(r-4.5-noble)MSnID_1.41.0.tar.gz(r-4.4-noble)
MSnID_1.41.0.tgz(r-4.4-emscripten)MSnID_1.41.0.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'))

Peer review:

Datasets:
  • msnidObj - Example mzIdenML File and MSnID Object

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

proteomicsmassspectrometryimmunooncology

5.06 score 57 scripts 635 downloads 1 mentions 26 exports 160 dependencies

Last updated 2 months agofrom:dc343c5a2c. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-winNOTENov 27 2024
R-4.5-linuxNOTENov 27 2024
R-4.4-winNOTENov 27 2024
R-4.4-macERRORNov 27 2024
R-4.3-winNOTENov 27 2024
R-4.3-macERRORNov 27 2024

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

Handling Modifications with MSnID

Rendered fromhandling_mods.Rnwusingutils::Sweaveon Nov 27 2024.

Last update: 2020-08-05
Started: 2020-07-14

MSnID Package for Handling MS/MS Identifications

Rendered frommsnid_vignette.Rnwusingutils::Sweaveon Nov 27 2024.

Last update: 2020-07-22
Started: 2014-09-27

Readme and manuals

Help Manual

Help pageTopics
MSnID: Utilities for Handling MS/MS IdentificationsMSnID-package
Non-redundant list of accession (protein) identifiersaccessions proteins
Annotates peptide sequences with modification symbolsadd_mod_symbol add_mod_symbol,MSnID-method
Filters the MS/MS identificationsapply_filter apply_filter,MSnID,character-method apply_filter,MSnID,MSnIDFilter-method
Counts the missing cleavage sites within the peptides sequenceassess_missed_cleavages
Checks if the peptide termini conforms with cleavage specificityassess_termini
Corrects wrong selection of monoisotopic peakcorrect_peak_selection
Filters the MS/MS identificationsevaluate_filter
Fetches conversion table form one type of identifiers to anotherfetch_conversion_table
Identification qualityid_quality
Eliminates Redundancy in Peptide-to-Protein Mappinginfer_parsimonious_accessions infer_parsimonious_accessions,MSnID-method
Maps the modifications to protein sequencemap_mod_sites map_mod_sites,MSnID-method
Computes error of the parent ion mass to charge measurementmass_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 Objectc_elegans msnidObj
Filter criteria optimization to maximize the number of identifications given the FDR upper thresholdoptimize_filter optimize_filter,MSnIDFilter,MSnID-method
Non-redundant list of peptidespeptides
Peptide-to-spectrum matchespsms psms<-
Populates MS/MS results table from mzIdentML filesread_mzIDs
Post-experimental recalibration of observed mass to charge ratiosrecalibrate
Changes accessions from one protein id to anotherremap_accessions remap_accessions,MSnID-method
Remapping entries in FASTA fileremap_fasta_entry_names
Lists modification masses in the MSnID objectreport_mods report_mods,MSnID-method