Mass Spectrometry Data on ExperimentHub

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Documentation for package ‘MsDataHub’ version 1.13.3

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

20171016_POOL_POS_1_105-134.mzML	AB Sciex LC-MS data files
20171016_POOL_POS_3_105-134.mzML	AB Sciex LC-MS data files
Ai2025	Ai et al (2025) single-cell data
Ai2025_aCMs_report.tsv	Ai et al (2025) single-cell data
Ai2025_iCMs_report.tsv	Ai et al (2025) single-cell data
benchmarkingDIA	DIA benchmarking data
benchmarkingDIA.tsv	DIA benchmarking data
Boekweg2022	Boekweg et al (2022) SCP, bulk and identification data
CEMS	CE-MS data files
CEMS_10ppm.mzML	CE-MS data files
CEMS_25ppm.mzML	CE-MS data files
Christoforou_2016_TMT_DDA_FragPipe_Fraction1_psm.tsv	Misc DDA and DIA datasets
Christoforou_2016_TMT_DDA_FragPipe_Fraction2_psm.tsv	Misc DDA and DIA datasets
Christoforou_2016_TMT_DDA_MaxQuant_evidence.txt	Misc DDA and DIA datasets
Christoforou_2016_TMT_DDA_sage_results.sage.tsv	Misc DDA and DIA datasets
Christoforou_2016_TMT_DDA_sage_tmt.tsv	Misc DDA and DIA datasets
contaminatants	Contaminant and cRAP databases
cptac	CPTAC label-free data
cptac_a_b_c_peptides.txt	CPTAC label-free data
cptac_a_b_peptides.txt	CPTAC label-free data
cptac_peptides.txt	CPTAC label-free data
cRAP	Contaminant and cRAP databases
crap	Contaminant and cRAP databases
crap_ccp.fasta	Contaminant and cRAP databases
crap_gpm.fasta	Contaminant and cRAP databases
crap_maxquant.fasta.gz	Contaminant and cRAP databases
D19_15um30cm_SC1.mzML	Boekweg et al (2022) SCP, bulk and identification data
D19_15um30cm_SC1.sage.tsv	Boekweg et al (2022) SCP, bulk and identification data
Derks_2022_plex_DIA_DIANN_report_subset.tsv	Misc DDA and DIA datasets
faahKO	Saghatelian et al. (2004) FAAH knockout LC/MS data
fdms3tmt11	MS3 SPS TMT data
fdms3tmt11.rda	MS3 SPS TMT data
FTICR	FTICR-MS data files
HAM004_641fE_14.11.07..Exp1.extracted.mzML	FTICR-MS data files
HAM004_641fE_14.11.07..Exp2.extracted.mzML	FTICR-MS data files
HAM004_641fE_14.11.07..Exp3.extracted.mzML	FTICR-MS data files
HAM004_641fE_14.11.07..Exp4.extracted.mzML	FTICR-MS data files
HAM004_641fE_14.11.07..Exp5.extracted.mzML	FTICR-MS data files
HAM005_641fE_14.11.07..Exp1.extracted.mzML	FTICR-MS data files
HAM005_641fE_14.11.07..Exp2.extracted.mzML	FTICR-MS data files
HAM005_641fE_14.11.07..Exp3.extracted.mzML	FTICR-MS data files
HAM005_641fE_14.11.07..Exp4.extracted.mzML	FTICR-MS data files
HAM005_641fE_14.11.07..Exp5.extracted.mzML	FTICR-MS data files
ko15.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
ko16.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
ko18.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
ko19.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
ko21.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
ko22.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
miscDdaDia	Misc DDA and DIA datasets
MRM	Multiple Reaction Monitoring mode (MRM) test files
MRM.standmix.5.mzML	Multiple Reaction Monitoring mode (MRM) test files
MS3TMT	MS3 SPS TMT data
MS3TMT10_01022016_32917-33481.mzML.gz	MS3 SPS TMT data
MS3TMT10_01022016_32917.33481.mzML.gz	MS3 SPS TMT data
MS3TMT11.mzML	MS3 SPS TMT data
MsDataHub	All MsDataHub datasets
OR11_20160122_PG_HeLa_CVB3_CT_A.mzML	Boekweg et al (2022) SCP, bulk and identification data
OR11_20160122_PG_HeLa_CVB3_CT_A.sage.tsv	Boekweg et al (2022) SCP, bulk and identification data
PestMix1_DDA.mzML	Triple TOF SWATH Data
PestMix1_SWATH.mzML	Triple TOF SWATH Data
PXD000001	PXD000001 Proteomics Data
Report.Derks2022.plexDIA	Derks 2022 plexDIA data
Report.Derks2022.plexDIA.tsv	Derks 2022 plexDIA data
sciex	AB Sciex LC-MS data files
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid	PXD000001 Proteomics Data
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML.gz	PXD000001 Proteomics Data
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid	PXD000001 Proteomics Data
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz	PXD000001 Proteomics Data
TripleTOF	Triple TOF SWATH Data
vanPuyvelde_2022_LFQ_DDA_FragPipe_A_1_psm.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_FragPipe_A_2_psm.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_FragPipe_A_3_psm.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_FragPipe_B_1_psm.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_FragPipe_B_2_psm.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_FragPipe_B_3_psm.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_MaxQuant_evidence.txt	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_MaxQuant_peptides.txt	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_MaxQuant_proteinGroups.txt	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_PEAKS_LFQ_report.csv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_sage_lfq.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DDA_sage_results.sage.tsv	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DIA_DIANN_report.parquet	Misc DDA and DIA datasets
vanPuyvelde_2022_LFQ_DIA_DIANN_report.tsv	Misc DDA and DIA datasets
wt15.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
wt16.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
wt18.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
wt19.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
wt21.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
wt22.CDF	Saghatelian et al. (2004) FAAH knockout LC/MS data
X20171016_POOL_POS_1_105.134.mzML	AB Sciex LC-MS data files
X20171016_POOL_POS_3_105.134.mzML	AB Sciex LC-MS data files