Data accompanying "Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using the scp package"

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.