{
  "_id": "6a4942c218cdde069385e7d8",
  "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",
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  "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": "2026-07-04 10:53:38 UTC",
    "User": "root"
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  "Author": "Laurent Gatto [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1520-2268>),\nKristina Gomoryova [ctb] (ORCID:\n<https://orcid.org/0000-0003-4407-3917>),\nJohannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),\nGuillaume Deflandre [ctb] (ORCID:\n<https://orcid.org/0009-0008-1257-2416>)",
  "Maintainer": "Laurent Gatto <laurent.gatto@uclouvain.be>",
  "_user": "bioc",
  "_type": "src",
  "_file": "MsDataHub_1.13.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/edebc8cfc2e4e5a43b6c3d4ff6fbda991ff272450870e4c8437275ca47147d72",
  "_filesize": 183824,
  "_sha256": "edebc8cfc2e4e5a43b6c3d4ff6fbda991ff272450870e4c8437275ca47147d72",
  "_expires": "2026-10-12T17:28:32.000Z",
  "_created": "2026-07-04T10:53:38.000Z",
  "_published": "2026-07-04T17:28:34.292Z",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 4
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28703634773",
  "_status": "success",
  "_upstream": "https://github.com/bioc/MsDataHub",
  "_commit": {
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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  "_maintainer": {
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    "email": "laurent.gatto@uclouvain.be",
    "login": "lgatto",
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    "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
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      "package": "utils",
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
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  "_tags": [],
  "_bioc": [
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  "_topics": [
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    "massspectrometry",
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  "_stars": 1,
  "_contributors": [
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_devurl": "https://github.com/rformassspectrometry/msdatahub",
  "_pkgdown": "https://rformassspectrometry.github.io/MsDataHub",
  "_searchresults": 94,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
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    "extra/NEWS.html",
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  "_homeurl": "https://github.com/rformassspectrometry/msdatahub",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Ai2025_aCMs_report.tsv",
    "Ai2025_iCMs_report.tsv",
    "benchmarkingDIA.tsv",
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    "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"
  ],
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    {
      "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"
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    },
    {
      "page": "Boekweg2022",
      "title": "Boekweg et al (2022) SCP, bulk and identification data",
      "topics": [
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        "D19_15um30cm_SC1.mzML",
        "D19_15um30cm_SC1.sage.tsv",
        "OR11_20160122_PG_HeLa_CVB3_CT_A.mzML",
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    },
    {
      "page": "cdf",
      "title": "MS data in CDF format",
      "topics": [
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        "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": [
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        "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",
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        "HAM005_641fE_14.11.07..Exp5.extracted.mzML"
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    },
    {
      "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",
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    "dbplyr",
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    "ExperimentHub",
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    "httr",
    "httr2",
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    "jsonlite",
    "KEGGREST",
    "lifecycle",
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    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "rappdirs",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "stringi",
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    "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",
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