Reference

All functions
Ai2025 Ai2025_aCMs_report.tsv Ai2025_iCMs_report.tsv	Ai et al (2025) single-cell data
CEMS CEMS_10ppm.mzML CEMS_25ppm.mzML	CE-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	FTICR-MS data files
MRM MRM.standmix.5.mzML	Multiple Reaction Monitoring mode (MRM) test files
MsDataHub()	All MsDataHub datasets
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	PXD000001 Proteomics Data
Report.Derks2022.plexDIA Report.Derks2022.plexDIA.tsv	Derks 2022 plexDIA data
TripleTOF PestMix1_DDA.mzML PestMix1_SWATH.mzML	Triple TOF SWATH Data
benchmarkingDIA benchmarkingDIA.tsv	DIA benchmarking data
cRAP crap contaminatants crap_ccp.fasta crap_gpm.fasta crap_maxquant.fasta.gz	Contaminant and cRAP databases
cdf ko15.CDF	MS data in CDF format
cptac cptac_a_b_c_peptides.txt cptac_a_b_peptides.txt cptac_peptides.txt	CPTAC label-free data
sciex 20171016_POOL_POS_1_105-134.mzML 20171016_POOL_POS_3_105-134.mzML X20171016_POOL_POS_1_105.134.mzML X20171016_POOL_POS_3_105.134.mzML	AB Sciex LC-MS data files