Datasets that have been applied to MSstats are shown below. All datasets (and more) are available in MassIVE.quant. To search for a dataset with an MSstats reanalysis, please review the datasets listed under the “Quant Reanalyses” page. All reanalysis containers start with the prefix “RMSV”. For more information please see the MassIVE.quant manuscript.

Workflow	Name	Description	Acquisition Type	Data Processing	Dataset	R script	PMID
MSstats	MSstatsBioData	R experiment package	various types	various tools	RData	check help file	DOI:10.18129/B9.bioc.MSstatsBioData
MSstats	ABRF iPRG 2015 study	Description, Spike-in proteins	Label-free LC-MS	Skyline	.zip	R script, annotation	27990823
MSstats	Controlled spike-in experiment	Description	Label-free LC-MS	SuperHirn	.csv	R script	17726677
MSstats	Controlled spike-in experiment	Description	SRM with labeled references	MultiQuant	.csv	R script	22190732
MSstats	Case-control investigation of ovarian cancer	Description	SRM with labeled references	MultiQuant	.csv	R script	22190732
MSstats	Time course investigation of S.cerevisiae	Description	SRM with labeled references	MultiQuant	.csv	R script	19664813
MSstats	CPTAC	Description	SRM with labeled references	Skyline	.csv	R script	19561596
LOB/LOD	Assay data	Description	SRM with labeled references	Skyline	.zip		26451657
MSstatsQC	CPTAC Study 9.1	System suitability testing results	SRM	Skyline	.csv	Shiny app + R script	25693799
MSstatsQC	QCloud QC dataset	Results for BSA QC samples	DDA	QCloud	.csv	Shiny app + R script
MSstatsQC	QCloud QC dataset	Results for BSA QC samples	SRM	QCloud	.csv	Shiny app + R script
MSstatsQC	QuiC iRT dataset	Results for spike-in iRT peptides	DIA	QuiC	.csv	Shiny app + R script	25724911

More datasets including data, R script and output are available in MSstats material github.