Package: MsDataHub 1.11.5

Laurent Gatto

MsDataHub: Mass Spectrometry Data on ExperimentHub

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

Authors:Laurent Gatto [aut, cre], Kristina Gomoryova [ctb], Johannes Rainer [aut], Guillaume Deflandre [ctb]

MsDataHub_1.11.5.tar.gz
MsDataHub_1.11.5.zip(r-4.7)MsDataHub_1.11.5.zip(r-4.6)MsDataHub_1.11.5.zip(r-4.5)
MsDataHub_1.11.5.tgz(r-4.6-any)MsDataHub_1.11.5.tgz(r-4.5-any)
MsDataHub_1.11.5.tar.gz(r-4.7-any)MsDataHub_1.11.5.tar.gz(r-4.6-any)
MsDataHub_1.11.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MsDataHub/json (API)
NEWS

# Install 'MsDataHub' in R:
install.packages('MsDataHub', repos = c('https://rformassspectrometry.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/msdatahub/issues

Pkgdown/docs site:https://rformassspectrometry.github.io

On BioConductor:MsDataHub-1.13.0(bioc 3.24)MsDataHub-1.12.0(bioc 3.23)

experimenthubsoftwaremassspectrometryproteomicsmetabolomicsbioconductordatamass-spectrometry

6.39 score 1 stars 1 packages 81 scripts 58 exports 57 dependencies

Last updated from:beb0a4d924. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK254
source / vignettesOK883
linux-release-x86_64OK270
macos-release-arm64OK182
macos-oldrel-arm64OK136
windows-develOK167
windows-releaseOK195
windows-oldrelOK175
wasm-releaseOK169

Exports:Ai2025_aCMs_report.tsvAi2025_iCMs_report.tsvbenchmarkingDIA.tsvCEMS_10ppm.mzMLCEMS_25ppm.mzMLChristoforou_2016_TMT_DDA_FragPipe_Fraction1_psm.tsvChristoforou_2016_TMT_DDA_FragPipe_Fraction2_psm.tsvChristoforou_2016_TMT_DDA_MaxQuant_evidence.txtChristoforou_2016_TMT_DDA_sage_results.sage.tsvChristoforou_2016_TMT_DDA_sage_tmt.tsvcptac_a_b_c_peptides.txtcptac_a_b_peptides.txtcptac_peptides.txtcrap_ccp.fastacrap_gpm.fastacrap_maxquant.fasta.gzD19_15um30cm_SC1.mzMLD19_15um30cm_SC1.sage.tsvDerks_2022_plex_DIA_DIANN_report_subset.tsvfdms3tmt11.rdaHAM004_641fE_14.11.07..Exp1.extracted.mzMLHAM004_641fE_14.11.07..Exp2.extracted.mzMLHAM004_641fE_14.11.07..Exp3.extracted.mzMLHAM004_641fE_14.11.07..Exp4.extracted.mzMLHAM004_641fE_14.11.07..Exp5.extracted.mzMLHAM005_641fE_14.11.07..Exp1.extracted.mzMLHAM005_641fE_14.11.07..Exp2.extracted.mzMLHAM005_641fE_14.11.07..Exp3.extracted.mzMLHAM005_641fE_14.11.07..Exp4.extracted.mzMLHAM005_641fE_14.11.07..Exp5.extracted.mzMLko15.CDFMRM.standmix.5.mzMLMS3TMT10_01022016_32917.33481.mzML.gzMS3TMT11.mzMLMsDataHubOR11_20160122_PG_HeLa_CVB3_CT_A.mzMLOR11_20160122_PG_HeLa_CVB3_CT_A.sage.tsvPestMix1_DDA.mzMLPestMix1_SWATH.mzMLReport.Derks2022.plexDIA.tsvTMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzidTMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gzvanPuyvelde_2022_LFQ_DDA_FragPipe_A_1_psm.tsvvanPuyvelde_2022_LFQ_DDA_FragPipe_A_2_psm.tsvvanPuyvelde_2022_LFQ_DDA_FragPipe_A_3_psm.tsvvanPuyvelde_2022_LFQ_DDA_FragPipe_B_1_psm.tsvvanPuyvelde_2022_LFQ_DDA_FragPipe_B_2_psm.tsvvanPuyvelde_2022_LFQ_DDA_FragPipe_B_3_psm.tsvvanPuyvelde_2022_LFQ_DDA_MaxQuant_evidence.txtvanPuyvelde_2022_LFQ_DDA_MaxQuant_peptides.txtvanPuyvelde_2022_LFQ_DDA_MaxQuant_proteinGroups.txtvanPuyvelde_2022_LFQ_DDA_PEAKS_LFQ_report.csvvanPuyvelde_2022_LFQ_DDA_sage_lfq.tsvvanPuyvelde_2022_LFQ_DDA_sage_results.sage.tsvvanPuyvelde_2022_LFQ_DIA_DIANN_report.parquetvanPuyvelde_2022_LFQ_DIA_DIANN_report.tsvX20171016_POOL_POS_1_105.134.mzMLX20171016_POOL_POS_3_105.134.mzML

Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrExperimentHubfastmapfilelockgenericsgluehttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml

Mass Spectrometry Data on ExperimentHub

Laurent Gatto

Rendered fromMsDataHub.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-03-20
Started: 2022-11-27

Readme and manuals

Help Manual

Help pageTopics
Ai et al (2025) single-cell dataAi2025 Ai2025_aCMs_report.tsv Ai2025_iCMs_report.tsv
DIA benchmarking databenchmarkingDIA benchmarkingDIA.tsv
Boekweg et al (2022) SCP, bulk and identification dataBoekweg2022 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
MS data in CDF formatcdf ko15.CDF
CE-MS data filesCEMS CEMS_10ppm.mzML CEMS_25ppm.mzML
CPTAC label-free datacptac cptac_a_b_c_peptides.txt cptac_a_b_peptides.txt cptac_peptides.txt
Contaminant and cRAP databasescontaminatants cRAP crap crap_ccp.fasta crap_gpm.fasta crap_maxquant.fasta.gz
FTICR-MS data filesFTICR 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
Misc DDA and DIA datasetsChristoforou_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
Multiple Reaction Monitoring mode (MRM) test filesMRM MRM.standmix.5.mzML
MS3 SPS TMT datafdms3tmt11 fdms3tmt11.rda MS3TMT MS3TMT10_01022016_32917-33481.mzML.gz MS3TMT10_01022016_32917.33481.mzML.gz MS3TMT11.mzML
All MsDataHub datasetsMsDataHub
PXD000001 Proteomics DataPXD000001 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
Derks 2022 plexDIA dataReport.Derks2022.plexDIA Report.Derks2022.plexDIA.tsv
AB Sciex LC-MS data files20171016_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
Triple TOF SWATH DataPestMix1_DDA.mzML PestMix1_SWATH.mzML TripleTOF