Data and scripts accompanying the paper Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using scp. d.zip contains raw MS data from samples run on timsTOF SCP. raw.zip contains raw MS data from samples run on orbitrap mass spectrometers (Orbitrap Fusion Lumos Tribrid and Exploris 240). mzML.zip contains raw MS data in mzML format from all samples. sage.zip contains output results from the sage software (results.sage.tsv and quant.tsv) as well as configuration files (results.json) for both orbitrap (cbio) and timsTOF (giga) data. sample_annotation.zip contains csv files with samples annotation for each acquisition batch and used to build the colData. example_subset.zip contains csv files for short example datasets displayed in the paper. scp.rds file contains the initial QFeatures object of the full dataset with 56 PSM sets corresponding to the 56 MS runs. build_QF_dataset.Rmd file is the script used to build the scp.rds file described above from sage outputs and sample annotation. These file descriptions are also available in the README.txt file.