{ "_id": "6a1ae7f31d7bb097a09f1861", "Package": "MsDataHub", "Title": "Mass Spectrometry Data on ExperimentHub", "Version": "1.13.0", "Authors@R": "c(person(given = \"Laurent\",\nfamily = \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1520-2268\")),\nperson(given = \"Kristina\",\nfamily = \"Gomoryova\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4407-3917\")),\nperson(given = \"Johannes\",\nfamily = \"Rainer\",\nemail = \"Johannes.Rainer@eurac.edu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Guillaume\",\nfamily = \"Deflandre\",\nemail = \"guillaume.deflandre@uclouvain.be\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0009-0008-1257-2416\")))", "Description": "The MsDataHub package uses the ExperimentHub\ninfrastructure to distribute raw mass spectrometry data files,\npeptide spectrum matches or quantitative data from proteomics\nand metabolomics experiments.", "License": "Artistic-2.0", "BugReports": "https://github.com/RforMassSpectrometry/MsDataHub/issues", "URL": "https://rformassspectrometry.github.io/MsDataHub", "biocViews": "ExperimentHubSoftware, MassSpectrometry, Proteomics,\nMetabolomics", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:00:15 UTC", "RemoteUrl": "https://github.com/bioc/MsDataHub", "RemoteRef": "HEAD", "RemoteSha": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:37:27 UTC", "User": "root" }, "Author": "Laurent Gatto [aut, cre] (ORCID:\n),\nKristina Gomoryova [ctb] (ORCID:\n),\nJohannes Rainer [aut] (ORCID: ),\nGuillaume Deflandre [ctb] (ORCID:\n)", "Maintainer": "Laurent Gatto ", "MD5sum": "4909c90791b1e0973b6cb4323b57629b", "_user": "bioc", "_type": "src", "_file": "MsDataHub_1.13.0.tar.gz", "_fileid": "190c40045da2635d7cc179dbf740f2c2cad7657d3551925490ba715eed4dfeda", "_filesize": 180241, "_sha256": "190c40045da2635d7cc179dbf740f2c2cad7657d3551925490ba715eed4dfeda", "_created": "2026-05-30T09:37:27.000Z", "_published": "2026-05-30T13:36:51.248Z", "_jobs": [ { "job": 78640122639, "time": 184, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307337731" }, { "job": 78640122642, "time": 226, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307341516" }, { "job": 78640122650, "time": 309, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307349399" }, { "job": 78640122636, "time": 162, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308562150" }, { "job": 78640122637, "time": 156, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308561865" }, { "job": 78639364569, "time": 409, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307231576" }, { "job": 78640122631, "time": 164, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307335667" }, { "job": 78640122654, "time": 171, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307338034" }, { "job": 78640122645, "time": 157, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307335892" }, { "job": 78640122646, "time": 171, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307337304" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MsDataHub", "_commit": { "id": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381215 }, "_maintainer": { "name": "Laurent Gatto", "email": "laurent.gatto@uclouvain.be", "login": "lgatto", "mastodon": "@lgatto@fediscience.org", "orcid": "0000-0002-1520-2268", "description": "Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.\n", "uuid": 384198 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "ExperimentHub", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ExperimentHubData", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "Spectra", "role": "Suggests" }, { "package": "mzR", "role": "Suggests" }, { "package": "PSMatch", "role": "Suggests" }, { "package": "QFeatures", "version": ">= 1.13.3", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-09", "n": 3 }, { "week": "2026-12", "n": 4 }, { "week": "2026-14", "n": 1 }, { "week": "2026-16", "n": 3 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.13.0", "bioc": "3.24" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23" } ], "_topics": [ "experimenthubsoftware", "massspectrometry", "proteomics", "metabolomics", "bioconductor", "data", "mass-spectrometry" ], "_stars": 1, "_contributors": [ { "user": "lgatto", "count": 92, "uuid": 384198 }, { "user": "guideflandre", "count": 12, "uuid": 37773040 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "jorainer", "count": 9, "uuid": 5506112 }, { "user": "kristinagomoryova", "count": 1, "uuid": 45943629 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 414, "source": "https://www.bioconductor.org/packages/stats/bioc/MsDataHub" }, "_devurl": "https://github.com/rformassspectrometry/msdatahub", "_pkgdown": "https://rformassspectrometry.github.io/MsDataHub", "_searchresults": 88, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MsDataHub.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rformassspectrometry/msdatahub", "_realowner": "bioc", "_cranurl": false, "_exports": [ "Ai2025_aCMs_report.tsv", "Ai2025_iCMs_report.tsv", "benchmarkingDIA.tsv", "CEMS_10ppm.mzML", "CEMS_25ppm.mzML", "Christoforou_2016_TMT_DDA_FragPipe_Fraction1_psm.tsv", "Christoforou_2016_TMT_DDA_FragPipe_Fraction2_psm.tsv", "Christoforou_2016_TMT_DDA_MaxQuant_evidence.txt", "Christoforou_2016_TMT_DDA_sage_results.sage.tsv", "Christoforou_2016_TMT_DDA_sage_tmt.tsv", "cptac_a_b_c_peptides.txt", "cptac_a_b_peptides.txt", "cptac_peptides.txt", "crap_ccp.fasta", "crap_gpm.fasta", "crap_maxquant.fasta.gz", "D19_15um30cm_SC1.mzML", "D19_15um30cm_SC1.sage.tsv", "Derks_2022_plex_DIA_DIANN_report_subset.tsv", "fdms3tmt11.rda", "HAM004_641fE_14.11.07..Exp1.extracted.mzML", "HAM004_641fE_14.11.07..Exp2.extracted.mzML", "HAM004_641fE_14.11.07..Exp3.extracted.mzML", "HAM004_641fE_14.11.07..Exp4.extracted.mzML", "HAM004_641fE_14.11.07..Exp5.extracted.mzML", "HAM005_641fE_14.11.07..Exp1.extracted.mzML", "HAM005_641fE_14.11.07..Exp2.extracted.mzML", "HAM005_641fE_14.11.07..Exp3.extracted.mzML", "HAM005_641fE_14.11.07..Exp4.extracted.mzML", "HAM005_641fE_14.11.07..Exp5.extracted.mzML", "ko15.CDF", "MRM.standmix.5.mzML", "MS3TMT10_01022016_32917.33481.mzML.gz", "MS3TMT11.mzML", "MsDataHub", "OR11_20160122_PG_HeLa_CVB3_CT_A.mzML", "OR11_20160122_PG_HeLa_CVB3_CT_A.sage.tsv", "PestMix1_DDA.mzML", "PestMix1_SWATH.mzML", "Report.Derks2022.plexDIA.tsv", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz", "vanPuyvelde_2022_LFQ_DDA_FragPipe_A_1_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_A_2_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_A_3_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_B_1_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_B_2_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_B_3_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_MaxQuant_evidence.txt", "vanPuyvelde_2022_LFQ_DDA_MaxQuant_peptides.txt", "vanPuyvelde_2022_LFQ_DDA_MaxQuant_proteinGroups.txt", "vanPuyvelde_2022_LFQ_DDA_PEAKS_LFQ_report.csv", "vanPuyvelde_2022_LFQ_DDA_sage_lfq.tsv", "vanPuyvelde_2022_LFQ_DDA_sage_results.sage.tsv", "vanPuyvelde_2022_LFQ_DIA_DIANN_report.parquet", "vanPuyvelde_2022_LFQ_DIA_DIANN_report.tsv", "X20171016_POOL_POS_1_105.134.mzML", "X20171016_POOL_POS_3_105.134.mzML" ], "_help": [ { "page": "Ai2025", "title": "Ai et al (2025) single-cell data", "topics": [ "Ai2025", "Ai2025_aCMs_report.tsv", "Ai2025_iCMs_report.tsv" ] }, { "page": "benchmarkingDIA", "title": "DIA benchmarking data", "topics": [ "benchmarkingDIA", "benchmarkingDIA.tsv" ] }, { "page": "Boekweg2022", "title": "Boekweg et al (2022) SCP, bulk and identification data", "topics": [ "Boekweg2022", "D19_15um30cm_SC1.mzML", "D19_15um30cm_SC1.sage.tsv", "OR11_20160122_PG_HeLa_CVB3_CT_A.mzML", "OR11_20160122_PG_HeLa_CVB3_CT_A.sage.tsv" ] }, { "page": "cdf", "title": "MS data in CDF format", "topics": [ "cdf", "ko15.CDF" ] }, { "page": "CEMS", "title": "CE-MS data files", "topics": [ "CEMS", "CEMS_10ppm.mzML", "CEMS_25ppm.mzML" ] }, { "page": "cptac", "title": "CPTAC label-free data", "topics": [ "cptac", "cptac_a_b_c_peptides.txt", "cptac_a_b_peptides.txt", "cptac_peptides.txt" ] }, { "page": "cRAP", "title": "Contaminant and cRAP databases", "topics": [ "contaminatants", "cRAP", "crap", "crap_ccp.fasta", "crap_gpm.fasta", "crap_maxquant.fasta.gz" ] }, { "page": "FTICR", "title": "FTICR-MS data files", "topics": [ "FTICR", "HAM004_641fE_14.11.07..Exp1.extracted.mzML", "HAM004_641fE_14.11.07..Exp2.extracted.mzML", "HAM004_641fE_14.11.07..Exp3.extracted.mzML", "HAM004_641fE_14.11.07..Exp4.extracted.mzML", "HAM004_641fE_14.11.07..Exp5.extracted.mzML", "HAM005_641fE_14.11.07..Exp1.extracted.mzML", "HAM005_641fE_14.11.07..Exp2.extracted.mzML", "HAM005_641fE_14.11.07..Exp3.extracted.mzML", "HAM005_641fE_14.11.07..Exp4.extracted.mzML", "HAM005_641fE_14.11.07..Exp5.extracted.mzML" ] }, { "page": "miscDdaDia", "title": "Misc DDA and DIA datasets", "topics": [ "Christoforou_2016_TMT_DDA_FragPipe_Fraction1_psm.tsv", "Christoforou_2016_TMT_DDA_FragPipe_Fraction2_psm.tsv", "Christoforou_2016_TMT_DDA_MaxQuant_evidence.txt", "Christoforou_2016_TMT_DDA_sage_results.sage.tsv", "Christoforou_2016_TMT_DDA_sage_tmt.tsv", "Derks_2022_plex_DIA_DIANN_report_subset.tsv", "miscDdaDia", "vanPuyvelde_2022_LFQ_DDA_FragPipe_A_1_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_A_2_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_A_3_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_B_1_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_B_2_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_FragPipe_B_3_psm.tsv", "vanPuyvelde_2022_LFQ_DDA_MaxQuant_evidence.txt", "vanPuyvelde_2022_LFQ_DDA_MaxQuant_peptides.txt", "vanPuyvelde_2022_LFQ_DDA_MaxQuant_proteinGroups.txt", "vanPuyvelde_2022_LFQ_DDA_PEAKS_LFQ_report.csv", "vanPuyvelde_2022_LFQ_DDA_sage_lfq.tsv", "vanPuyvelde_2022_LFQ_DDA_sage_results.sage.tsv", "vanPuyvelde_2022_LFQ_DIA_DIANN_report.parquet", "vanPuyvelde_2022_LFQ_DIA_DIANN_report.tsv" ] }, { "page": "MRM", "title": "Multiple Reaction Monitoring mode (MRM) test files", "topics": [ "MRM", "MRM.standmix.5.mzML" ] }, { "page": "MS3TMT", "title": "MS3 SPS TMT data", "topics": [ "fdms3tmt11", "fdms3tmt11.rda", "MS3TMT", "MS3TMT10_01022016_32917-33481.mzML.gz", "MS3TMT10_01022016_32917.33481.mzML.gz", "MS3TMT11.mzML" ] }, { "page": "MsDataHub", "title": "All MsDataHub datasets", "topics": [ "MsDataHub" ] }, { "page": "PXD000001", "title": "PXD000001 Proteomics Data", "topics": [ "PXD000001", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML.gz", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid", "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz" ] }, { "page": "Report.Derks2022.plexDIA", "title": "Derks 2022 plexDIA data", "topics": [ "Report.Derks2022.plexDIA", "Report.Derks2022.plexDIA.tsv" ] }, { "page": "sciex", "title": "AB Sciex LC-MS data files", "topics": [ "20171016_POOL_POS_1_105-134.mzML", "20171016_POOL_POS_3_105-134.mzML", "sciex", "X20171016_POOL_POS_1_105.134.mzML", "X20171016_POOL_POS_3_105.134.mzML" ] }, { "page": "TripleTOF", "title": "Triple TOF SWATH Data", "topics": [ "PestMix1_DDA.mzML", "PestMix1_SWATH.mzML", "TripleTOF" ] } ], "_readme": "https://github.com/bioc/MsDataHub/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "AnnotationHub", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "ExperimentHub", "fastmap", "filelock", "generics", "glue", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector", "yaml" ], "_vignettes": [ { "source": "MsDataHub.Rmd", "filename": "MsDataHub.html", "title": "Mass Spectrometry Data on ExperimentHub", "author": "Laurent Gatto", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Available data", "TripleTOF", "sciex", "PXD000001", "CPTAC", "FAAH KO", "DIA-NN software outputs", "DIA-NN single-cell proteomics reports", "Proteomics contaminant databases", "FTICR-MS direct injection MS data", "MRM data file", "CE-MS data", "TMT MS3 SPS data", "Adding data to MsDataHub", "Session information" ], "created": "2022-11-27 21:11:59", "modified": "2026-03-20 17:59:49", "commits": 15 } ], "_score": 6.500785172917456, "_indexed": true, "_nocasepkg": "msdatahub", "_universes": [ "bioc", "lgatto", "rformassspectrometry" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13.0", "date": "2026-05-30T09:55:06.000Z", "distro": "noble", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "8f5231dea4765103a43c39c6d57cba215e9ae8b333aabe0b614286d03c0be572", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.6.0", "os": "linux", "version": "1.13.0", "date": "2026-05-30T09:56:24.000Z", "distro": "noble", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "9efa1dd78ac2aea4498d6599a63948b8d7d61d8bc768556aaa36b204d1a839d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.5.3", "os": "mac", "version": "1.13.0", "date": "2026-05-30T13:35:39.000Z", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "647f12e0f3173c556fa79564eefdce9c448e0d8196356b5ed75ee36c8554c6c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.6.0", "os": "mac", "version": "1.13.0", "date": "2026-05-30T13:35:38.000Z", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "fd333c1aaa2d83e807ecbf96d972c88ac3e2be7b41030cebb390e5bfc17baf3f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.6.0", "os": "wasm", "version": "1.13.0", "date": "2026-05-30T09:55:12.000Z", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "3c69a0ed84c2cb77bea5c9909bb6a5c5d19346474c61df352eb9aa2e495bb7a5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.7.0", "os": "win", "version": "1.13.0", "date": "2026-05-30T09:54:13.000Z", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "fe785465d2c8a9fac1f47da5b962a80abf95e3caa7b42327f5fb9348e06065b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.5.3", "os": "win", "version": "1.13.0", "date": "2026-05-30T09:54:14.000Z", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "46276d60e7083915e37ec7993e5a5a7c23887d6014bbec33bd280a913e092c7e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" }, { "r": "4.6.0", "os": "win", "version": "1.13.0", "date": "2026-05-30T09:54:03.000Z", "commit": "7b93f891acccdbf2e65c2fa38510a41e9c8c956d", "fileid": "7f30981a0285ca3b5acaab19a72bfc35f61afdb6417b4d987f5f05253decbe45", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675730821" } ] }