The MsDataHub package provides example mass spectrometry data, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.
The MsDataHub() function returns a data.frame with all the
annotated datasets provided in the package. For details on these
individual datasets, refer to their respective manual pages.
See the vignette and the respective manuals pages for more details about the package and the data themselves.
MsDataHub()A data.frame describing the data available in
MsDataHub.
MsDataHub()
#> Title
#> 1 ko15.CDF
#> 2 cptac_a_b_c_peptides.txt
#> 3 cptac_a_b_peptides.txt
#> 4 cptac_peptides.txt
#> 5 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid
#> 6 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz
#> 7 X20171016_POOL_POS_1_105.134.mzML
#> 8 X20171016_POOL_POS_3_105.134.mzML
#> 9 PestMix1_DDA.mzML
#> 10 PestMix1_SWATH.mzML
#> 11 benchmarkingDIA.tsv
#> 12 Report.Derks2022.plexDIA.tsv
#> 13 Ai2025_aCMs_report.tsv
#> 14 Ai2025_iCMs_report.tsv
#> Description
#> 1 Raw metabolomics MS file in netCDF format. See ?ko15.CDF for details.
#> 2 Conditions A, B and C of the CPTAC quantitative proteomics data (tab-delimited format). See ?cptac for details.
#> 3 Conditions A and B of the CPTAC quantitative proteomics data (tab-delimited format). See ?cptac for details.
#> 4 CPTAC quantitative proteomics data (tab-delimited format). See ?cptac for details.
#> 5 Peptide spectrum matches from the PDX000001 experiment. See ?PXD000001 for details.
#> 6 Raw MS data from the PDX000001 experiment, in mzML format. See ?PXD000001 for details.
#> 7 AB Sciex LC-MS data file (injection index 1), in mzML format. See ?sciex for details.
#> 8 AB Sciex LC-MS data file (injection index 19), in mzML format. See ?sciex for details.
#> 9 Triple TOF DDA raw data, in mzML format. See ?TripleTOF for details.
#> 10 Triple TOF SWATH raw data, in mzML format. See ?TripleTOF for details.
#> 11 Output of DIA-NN software (report.tsv)
#> 12 Derk et al. (2022) single-cell proteomics plexDIA results (DIA-NN report.tsv).
#> 13 Ai et al. (2025) Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts.
#> 14 Ai et al. (2025) Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts.
#> BiocVersion Genome SourceType
#> 1 3.17 NA CDF
#> 2 3.17 NA TXT
#> 3 3.17 NA TXT
#> 4 3.17 NA TXT
#> 5 3.17 NA mzid
#> 6 3.17 NA mzML
#> 7 3.17 NA mzML
#> 8 3.17 NA mzML
#> 9 3.17 NA mzML
#> 10 3.17 NA mzML
#> 11 3.17 NA TSV
#> 12 3.19 NA TSV
#> 13 3.21 NA TSV
#> 14 3.21 NA TSV
#> SourceUrl
#> 1 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 2 https://uclouvain-cbio.github.io/WSBIM2122/data/cptac_a_b_c_peptides.txt
#> 3 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 4 https://raw.githubusercontent.com/statOmics/PDA/data/quantification/fullCptacDatasSetNotForTutorial/peptides.txt
#> 5 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 6 https://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/
#> 7 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 8 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 9 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 10 https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html
#> 11 https://zenodo.org/records/8063173
#> 12 https://drive.google.com/drive/folders/1pUC2zgXKtKYn22mlor0lmUDK0frgwL_-
#> 13 ftp://massive.ucsd.edu/v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/aCMs/report.tsv
#> 14 ftp://massive.ucsd.edu/v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/iCMs/report1.tsv
#> SourceVersion Species TaxonomyId Coordinate_1_based
#> 1 1 Mus musculus 10090 NA
#> 2 1 Saccharomyces cerevisiae 4932 NA
#> 3 1 Saccharomyces cerevisiae 4932 NA
#> 4 1 Saccharomyces cerevisiae 4932 NA
#> 5 1 Erwinia carotovora 554 NA
#> 6 1 Erwinia carotovora 554 NA
#> 7 1 Homo sapiens 9606 NA
#> 8 1 Homo sapiens 9606 NA
#> 9 1 NA NA
#> 10 1 NA NA
#> 11 1 Homo sapiens 9606 NA
#> 12 1 Homo sapiens 9606 NA
#> 13 1 Homo sapiens 9606 NA
#> 14 1 Homo sapiens 9606 NA
#> DataProvider Maintainer RDataClass
#> 1 NA Laurent Gatto <laurent.gatto@uclouvain.be> Spectra
#> 2 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> 3 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> 4 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> 5 NA Laurent Gatto <laurent.gatto@uclouvain.be> Spectra
#> 6 NA Laurent Gatto <laurent.gatto@uclouvain.be> PSM
#> 7 NA Laurent Gatto <laurent.gatto@uclouvain.be> Spectra
#> 8 NA Laurent Gatto <laurent.gatto@uclouvain.be> Spectra
#> 9 NA Laurent Gatto <laurent.gatto@uclouvain.be> Spectra
#> 10 NA Laurent Gatto <laurent.gatto@uclouvain.be> Spectra
#> 11 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> 12 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> 13 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> 14 NA Laurent Gatto <laurent.gatto@uclouvain.be> data.frame
#> DispatchClass Location_Prefix
#> 1 FilePath
#> 2 FilePath
#> 3 FilePath
#> 4 FilePath
#> 5 FilePath
#> 6 FilePath
#> 7 FilePath
#> 8 FilePath
#> 9 FilePath
#> 10 FilePath
#> 11 FilePath https://zenodo.org/
#> 12 FilePath https://zenodo.org/
#> 13 FilePath ftp://massive.ucsd.edu/
#> 14 FilePath ftp://massive.ucsd.edu/
#> RDataPath
#> 1 MsDataHub/cdf/ko15.CDF
#> 2 MsDataHub/cptac/cptac_a_b_c_peptides.txt
#> 3 MsDataHub/cptac/cptac_a_b_peptides.txt
#> 4 MsDataHub/cptac/cptac_peptides.txt
#> 5 MsDataHub/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid
#> 6 MsDataHub/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML.gz
#> 7 MsDataHub/sciex/20171016_POOL_POS_1_105-134.mzML
#> 8 MsDataHub/sciex/20171016_POOL_POS_3_105-134.mzML
#> 9 MsDataHub/TripleTOF-SWATH/PestMix1_DDA.mzML
#> 10 MsDataHub/TripleTOF-SWATH/PestMix1_SWATH.mzML
#> 11 record/8063173/files/benchmarkingDIA.tsv
#> 12 records/10938597/files/Report-Derks2022-plexDIA.tsv
#> 13 v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/aCMs/report.tsv
#> 14 v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/iCMs/report1.tsv
#> Tags
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 NA
#> 7 NA
#> 8 NA
#> 9 NA
#> 10 NA
#> 11 NA
#> 12 NA
#> 13 NA
#> 14 NA