"Title","Description","BiocVersion","Genome","SourceType","SourceUrl","SourceVersion","Species","TaxonomyId","Coordinate_1_based","DataProvider","Maintainer","RDataClass","DispatchClass","Location_Prefix","RDataPath","Tags"
"ko15.CDF","Raw metabolomics MS file in netCDF format. See ?ko15.CDF for details.","3.17","","CDF","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","Mus musculus","10090","","","Laurent Gatto <laurent.gatto@uclouvain.be>","Spectra","FilePath","","MsDataHub/cdf/ko15.CDF",""
"cptac_a_b_c_peptides.txt","Conditions A, B and C of the CPTAC quantitative proteomics data (tab-delimited format). See ?cptac for details.","3.17","","TXT","https://uclouvain-cbio.github.io/WSBIM2122/data/cptac_a_b_c_peptides.txt","1.0","Saccharomyces cerevisiae","4932","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","","MsDataHub/cptac/cptac_a_b_c_peptides.txt",""
"cptac_a_b_peptides.txt","Conditions A and B of the CPTAC quantitative proteomics data (tab-delimited format). See ?cptac for details.","3.17","","TXT","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","Saccharomyces cerevisiae","4932","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","","MsDataHub/cptac/cptac_a_b_peptides.txt",""
"cptac_peptides.txt","CPTAC quantitative proteomics data (tab-delimited format). See ?cptac for details.","3.17","","TXT","https://raw.githubusercontent.com/statOmics/PDA/data/quantification/fullCptacDatasSetNotForTutorial/peptides.txt","1.0","Saccharomyces cerevisiae","4932","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","","MsDataHub/cptac/cptac_peptides.txt",""
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid","Peptide spectrum matches from the PDX000001 experiment. See ?PXD000001 for details.","3.17","","mzid","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","Erwinia carotovora","554","","","Laurent Gatto <laurent.gatto@uclouvain.be>","Spectra","FilePath","","MsDataHub/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid",""
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz","Raw MS data from the PDX000001 experiment, in mzML format. See ?PXD000001 for details.","3.17","","mzML","https://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/","1.0","Erwinia carotovora","554","","","Laurent Gatto <laurent.gatto@uclouvain.be>","PSM","FilePath","","MsDataHub/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML.gz",""
"X20171016_POOL_POS_1_105.134.mzML","AB Sciex LC-MS data file (injection index 1), in mzML format. See ?sciex for details.","3.17","","mzML","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","Homo sapiens","9606","","","Laurent Gatto <laurent.gatto@uclouvain.be>","Spectra","FilePath","","MsDataHub/sciex/20171016_POOL_POS_1_105-134.mzML",""
"X20171016_POOL_POS_3_105.134.mzML","AB Sciex LC-MS data file (injection index 19), in mzML format. See ?sciex for details.","3.17","","mzML","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","Homo sapiens","9606","","","Laurent Gatto <laurent.gatto@uclouvain.be>","Spectra","FilePath","","MsDataHub/sciex/20171016_POOL_POS_3_105-134.mzML",""
"PestMix1_DDA.mzML","Triple TOF DDA raw data, in mzML format. See ?TripleTOF for details.","3.17","","mzML","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","","","","","Laurent Gatto <laurent.gatto@uclouvain.be>","Spectra","FilePath","","MsDataHub/TripleTOF-SWATH/PestMix1_DDA.mzML",""
"PestMix1_SWATH.mzML","Triple TOF SWATH raw data, in mzML format. See ?TripleTOF for details.","3.17","","mzML","https://bioconductor.org/packages/3.16/data/experiment/html/msdata.html","1.0","","","","","Laurent Gatto <laurent.gatto@uclouvain.be>","Spectra","FilePath","","MsDataHub/TripleTOF-SWATH/PestMix1_SWATH.mzML",""
"benchmarkingDIA.tsv","Output of DIA-NN software (report.tsv)","3.17","","TSV","https://zenodo.org/records/8063173","1.0","Homo sapiens","9606","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","https://zenodo.org/","record/8063173/files/benchmarkingDIA.tsv",""
"Report.Derks2022.plexDIA.tsv","Derk et al. (2022) single-cell proteomics plexDIA results (DIA-NN report.tsv).","3.19","","TSV","https://drive.google.com/drive/folders/1pUC2zgXKtKYn22mlor0lmUDK0frgwL_-","1.0","Homo sapiens","9606","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","https://zenodo.org/","records/10938597/files/Report-Derks2022-plexDIA.tsv",""
"Ai2025_aCMs_report.tsv","Ai et al. (2025) Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts.","3.21","","TSV","ftp://massive.ucsd.edu/v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/aCMs/report.tsv","1.0","Homo sapiens","9606","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","ftp://massive.ucsd.edu/","v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/aCMs/report.tsv",""
"Ai2025_iCMs_report.tsv","Ai et al. (2025) Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts.","3.21","","TSV","ftp://massive.ucsd.edu/v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/iCMs/report1.tsv","1.0","Homo sapiens","9606","","","Laurent Gatto <laurent.gatto@uclouvain.be>","data.frame","FilePath","ftp://massive.ucsd.edu/","v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/iCMs/report1.tsv",""
"crap_gpm.fasta","common Repository of Adventitious Proteins (cRAP) from the Global Proteome Machine (GPM)","3.21","","FASTA","https://zenodo.org/records/15115102/files/crap_gpm.fasta","1.0","","","","","Laurent Gatto <laurent.gatto@uclouvain.be>","AAStringSet","FilePath","https://zenodo.org/","records/15115102/files/crap_gpm.fasta",""
"crap_ccp.fasta","common Repository of Adventitious Proteins (cRAP) from the Cambridge Centre for Proteomics (CCP)","3.21","","FASTA","https://zenodo.org/records/15115102/files/crap_ccp.fasta","1.0","","","","","Laurent Gatto <laurent.gatto@uclouvain.be>","AAStringSet","FilePath","https://zenodo.org/","records/15115102/files/crap_ccp.fasta",""
"crap_maxquant.fasta.gz","MaxQuant's contaminant database","3.21","","FASTA","https://zenodo.org/records/15115102/files/crap_maxquant.fasta.gz","1.0","","","","","Laurent Gatto <laurent.gatto@uclouvain.be>","AAStringSet","FilePath","https://zenodo.org/","records/15115102/files/crap_maxquant.fasta.gz",""
