{ "_id": "6a216688cd65a98ecbd35b2c", "Package": "MSnID", "Type": "Package", "Title": "Utilities for Exploration and Assessment of Confidence of LC-MSn\nProteomics Identifications", "Version": "1.47.0", "Author": "Vlad Petyuk with contributions from Laurent Gatto", "Maintainer": "Vlad Petyuk ", "Description": "Extracts MS/MS ID data from mzIdentML (leveraging mzID\npackage) or text files. After collating the search results from\nmultiple datasets it assesses their identification quality and\noptimize filtering criteria to achieve the maximum number of\nidentifications while not exceeding a specified false discovery\nrate. Also contains a number of utilities to explore the MS/MS\nresults and assess missed and irregular enzymatic cleavages,\nmass measurement accuracy, etc.", "License": "Artistic-2.0", "LazyData": "yes", "biocViews": "Proteomics, MassSpectrometry, ImmunoOncology", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:47 UTC", "RemoteUrl": "https://github.com/bioc/MSnID", "RemoteRef": "HEAD", "RemoteSha": "322e5b848d9d11931142d6d1d2ea753c2946d092", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 11:20:11 UTC", "User": "root" }, "MD5sum": "0581ebb7979c6bd60e6dd3159dbf4579", "_user": "bioc", "_type": "src", "_file": "MSnID_1.47.0.tar.gz", "_fileid": "1cfb680d92063c1bf65d39cb4a6b414e003eb10651eab88a56318002d9a8c906", "_filesize": 3297558, "_sha256": "1cfb680d92063c1bf65d39cb4a6b414e003eb10651eab88a56318002d9a8c906", "_created": "2026-06-04T11:20:11.000Z", "_published": "2026-06-04T11:50:32.826Z", "_jobs": [ { "job": 79507743873, "time": 218, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7410171712" }, { "job": 79507743878, "time": 560, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7410277817" }, { "job": 79507743883, "time": 717, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7410329430" }, { "job": 79507743908, "time": 344, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7410641421" }, { "job": 79507743882, "time": 323, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7410630116" }, { "job": 79506591030, "time": 437, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7410102402" }, { "job": 79507743874, "time": 183, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7410160848" }, { "job": 79507743881, "time": 690, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7410321554" }, { "job": 79507743919, "time": 663, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7410312746" }, { "job": 79507743933, "time": 587, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7410286450" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MSnID", "_commit": { "id": "322e5b848d9d11931142d6d1d2ea753c2946d092", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379987 }, "_maintainer": { "name": "Vlad Petyuk", "email": "petyuk@gmail.com", "login": "vladpetyuk", "description": "senior scientist at PNNL", "uuid": 4207635 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Rcpp", "role": "Depends" }, { "package": "MSnbase", "version": ">= 1.12.1", "role": "Imports" }, { "package": "mzID", "version": ">= 1.3.5", "role": "Imports" }, { "package": "R.cache", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "iterators", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "ProtGenerics", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "mzR", "role": "Imports" }, { "package": "BiocStyle", "role": "Imports" }, { "package": "msmsTests", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "RUnit", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "AnnotationHub", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "xtable", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-06", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23" } ], "_topics": [ "proteomics", "massspectrometry", "immunooncology" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 667, "source": "https://www.bioconductor.org/packages/stats/bioc/MSnID" }, "_mentions": 1, "_searchresults": 74, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MSnID.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "accessions", "add_mod_symbol", "apply_filter", "assess_missed_cleavages", "assess_termini", "correct_peak_selection", "evaluate_filter", "fetch_conversion_table", "id_quality", "infer_parsimonious_accessions", "map_mod_sites", "mass_measurement_error", "MSnID", "MSnIDFilter", "optimize_filter", "peptides", "proteins", "psms", "psms<-", "read_mzIDs", "recalibrate", "remap_accessions", "remap_fasta_entry_names", "report_mods", "show", "update" ], "_datasets": [ { "name": "msnidObj", "title": "Example mzIdenML File and MSnID Object", "object": "c_elegans", "class": [ "MSnID" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "MSnID-package", "title": "MSnID: Utilities for Handling MS/MS Identifications", "topics": [ "MSnID-package" ] }, { "page": "accessions", "title": "Non-redundant list of accession (protein) identifiers", "topics": [ "accessions", "proteins" ] }, { "page": "add_mod_symbol", "title": "Annotates peptide sequences with modification symbols", "topics": [ "add_mod_symbol", "add_mod_symbol,MSnID-method" ] }, { "page": "apply_filter", "title": "Filters the MS/MS identifications", "topics": [ "apply_filter", "apply_filter,MSnID,character-method", "apply_filter,MSnID,MSnIDFilter-method" ] }, { "page": "assess_missed_cleavages", "title": "Counts the missing cleavage sites within the peptides sequence", "topics": [ "assess_missed_cleavages" ] }, { "page": "assess_termini", "title": "Checks if the peptide termini conforms with cleavage specificity", "topics": [ "assess_termini" ] }, { "page": "correct_peak_selection", "title": "Corrects wrong selection of monoisotopic peak", "topics": [ "correct_peak_selection" ] }, { "page": "evaluate_filter", "title": "Filters the MS/MS identifications", "topics": [ "evaluate_filter" ] }, { "page": "fetch_conversion_table", "title": "Fetches conversion table form one type of identifiers to another", "topics": [ "fetch_conversion_table" ] }, { "page": "id_quality", "title": "Identification quality", "topics": [ "id_quality" ] }, { "page": "infer_parsimonious_accessions", "title": "Eliminates Redundancy in Peptide-to-Protein Mapping", "topics": [ "infer_parsimonious_accessions", "infer_parsimonious_accessions,MSnID-method" ] }, { "page": "map_mod_sites", "title": "Maps the modifications to protein sequence", "topics": [ "map_mod_sites", "map_mod_sites,MSnID-method" ] }, { "page": "mass_measurement_error", "title": "Computes error of the parent ion mass to charge measurement", "topics": [ "mass_measurement_error" ] }, { "page": "MSnID-class", "title": "The \"MSnID\" Class for Mass Spectrometry Based Proteomics Identification Data", "topics": [ "$,MSnID-method", "$<-,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" ] }, { "page": "MSnIDFilter-class", "title": "The \"MSnIDFilter\" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.", "topics": [ "$,MSnIDFilter-method", "$<-,MSnIDFilter-method", "as.numeric,MSnIDFilter-method", "class:MSnIDFilter", "length,MSnIDFilter-method", "MSnIDFilter", "MSnIDFilter-class", "names,MSnIDFilter-method", "show,MSnIDFilter-method", "update,MSnIDFilter-method" ] }, { "page": "data", "title": "Example mzIdenML File and MSnID Object", "topics": [ "c_elegans", "msnidObj" ] }, { "page": "optimize_filter", "title": "Filter criteria optimization to maximize the number of identifications given the FDR upper threshold", "topics": [ "optimize_filter", "optimize_filter,MSnIDFilter,MSnID-method" ] }, { "page": "peptides", "title": "Non-redundant list of peptides", "topics": [ "peptides" ] }, { "page": "psms", "title": "Peptide-to-spectrum matches", "topics": [ "psms", "psms<-" ] }, { "page": "read_mzIDs", "title": "Populates MS/MS results table from mzIdentML files", "topics": [ "read_mzIDs" ] }, { "page": "recalibrate", "title": "Post-experimental recalibration of observed mass to charge ratios", "topics": [ "recalibrate" ] }, { "page": "remap_accessions-method", "title": "Changes accessions from one protein id to another", "topics": [ "remap_accessions", "remap_accessions,MSnID-method" ] }, { "page": "remap_fasta_entry_names", "title": "Remapping entries in FASTA file", "topics": [ "remap_fasta_entry_names" ] }, { "page": "report_mods", "title": "Lists modification masses in the MSnID object", "topics": [ "report_mods", "report_mods,MSnID-method" ] } ], "_readme": "https://github.com/bioc/MSnID/raw/HEAD/README.md", "_rundeps": [ "abind", "affy", "affyio", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "BiocStyle", "BiocVersion", "Biostrings", "bit", "bit64", "bitops", "blob", "bookdown", "bslib", "cachem", "caTools", "cli", "clue", "cluster", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "edgeR", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gplots", "gtable", "gtools", "highr", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "MALDIquant", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "msmsEDA", "msmsTests", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "png", "preprocessCore", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "qvalue", "R.cache", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "RSQLite", "RUnit", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xfun", "XML", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "handling_mods.Rnw", "filename": "handling_mods.pdf", "title": "Handling Modifications with MSnID", "engine": "utils::Sweave", "headings": [], "created": "2020-07-14 06:11:52", "modified": "2020-08-05 01:42:15", "commits": 4 }, { "source": "msnid_vignette.Rnw", "filename": "msnid_vignette.pdf", "title": "MSnID Package for Handling MS/MS Identifications", "engine": "utils::Sweave", "headings": [], "created": "2014-09-27 00:29:42", "modified": "2020-07-22 00:11:15", "commits": 4 } ], "_score": 5.346352974450639, "_indexed": true, "_nocasepkg": "msnid", "_universes": [ "bioc", "vladpetyuk" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-06-04T11:24:44.000Z", "distro": "noble", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "b61e1050cc5764f703146055617a15353438ddd3c369dd25f9120833d4a4ba18", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-06-04T11:24:48.000Z", "distro": "noble", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "7c5392a2e0732cfdc6e7737204f69b8c7d95e8faaca3eae38cc403286b3ad05f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-06-04T11:45:49.000Z", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "66a209df3adf4e3de5423b8c6e1bf0744ac404b89cdbeb13018ca2d29377116f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-06-04T11:45:29.000Z", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "812c235109f6946b36788e65b6ad468152b2488815c3afc3b8c9785cfd8a0c61", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-06-04T11:24:08.000Z", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "ba3d45459d43beb8cd637172945eacca564dd88facb7bbecae27623603a8a5ea", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-06-04T11:23:28.000Z", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "457a782339c14b77a02fc301ba68df3696ee8b5bdd9a7af0bae6823efe6aeeaa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-06-04T11:22:41.000Z", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "0459b45739a3b6c95877d98f5a7234cce7ef7e21b4c831d18da6cfa0e7a8c696", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" }, { "r": "4.6.0", "os": "win", "version": "1.47.0", "date": "2026-06-04T11:22:28.000Z", "commit": "322e5b848d9d11931142d6d1d2ea753c2946d092", "fileid": "8cb6937ff3108b4febb0b0aef079ab0aa38642eb139bd543f17c53882e3f7a0d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948250357" } ] }