## SCoPE2 data processed to ASCII text matrices

• Peptides-raw.csv
• Peptides x single cells at 1% FDR. The first 2 columns list the corresponding protein identifiers and peptide sequences and each subsequent column corresponds to a single cell. Peptide identification is based on spectra analyzed by MaxQuant and is enhanced by using DART-ID to incorporate retention time information. See Specht et al., 2019 for details.

• Proteins-processed.csv
• Proteins x single cells at 1% FDR, imputed and batch corrected.

• Cells.csv
• Annotation x single cells. Each column corresponds to a single cell and the rows include relevant metadata, such as, cell type if known, measurements from the isolation of the cell, and derivative quantities, i.e., rRI, CVs, reliability.

## SCoPE2 RAW data and search results from MaxQuant

• MassIVE Repository: