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
Package: MsDataHub 1.13.0
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:
MsDataHub_1.13.0.tar.gz
MsDataHub_1.13.0.zip(r-4.7)MsDataHub_1.13.0.zip(r-4.6)MsDataHub_1.13.0.zip(r-4.5)
MsDataHub_1.13.0.tgz(r-4.6-any)MsDataHub_1.13.0.tgz(r-4.5-any)
MsDataHub_1.13.0.tar.gz(r-4.7-any)MsDataHub_1.13.0.tar.gz(r-4.6-any)
MsDataHub_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MsDataHub/json (API)
| # Install 'MsDataHub' in R: |
| install.packages('MsDataHub', repos = c('https://bioc.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
Last updated from:7b93f891ac. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 194 | ||
| linux-devel-x86_64 | OK | 273 | ||
| source / vignettes | OK | 744 | ||
| linux-release-x86_64 | OK | 289 | ||
| macos-release-arm64 | OK | 131 | ||
| macos-oldrel-arm64 | OK | 142 | ||
| windows-devel | OK | 153 | ||
| windows-release | OK | 163 | ||
| windows-oldrel | OK | 156 | ||
| wasm-release | OK | 195 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Ai et al (2025) single-cell data | Ai2025 Ai2025_aCMs_report.tsv Ai2025_iCMs_report.tsv |
| DIA benchmarking data | benchmarkingDIA benchmarkingDIA.tsv |
| Boekweg et al (2022) SCP, bulk and identification data | 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 |
| MS data in CDF format | cdf ko15.CDF |
| CE-MS data files | CEMS CEMS_10ppm.mzML CEMS_25ppm.mzML |
| CPTAC label-free data | cptac cptac_a_b_c_peptides.txt cptac_a_b_peptides.txt cptac_peptides.txt |
| Contaminant and cRAP databases | contaminatants cRAP crap crap_ccp.fasta crap_gpm.fasta crap_maxquant.fasta.gz |
| FTICR-MS data files | 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 |
| Misc DDA and DIA datasets | 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 |
| Multiple Reaction Monitoring mode (MRM) test files | MRM MRM.standmix.5.mzML |
| MS3 SPS TMT data | fdms3tmt11 fdms3tmt11.rda MS3TMT MS3TMT10_01022016_32917-33481.mzML.gz MS3TMT10_01022016_32917.33481.mzML.gz MS3TMT11.mzML |
| All MsDataHub datasets | MsDataHub |
| PXD000001 Proteomics Data | 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 |
| Derks 2022 plexDIA data | Report.Derks2022.plexDIA Report.Derks2022.plexDIA.tsv |
| AB Sciex LC-MS data files | 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 |
| Triple TOF SWATH Data | PestMix1_DDA.mzML PestMix1_SWATH.mzML TripleTOF |
