## Article: Huffman et al, 2022, version 1

### Single-cell proteomics method: pSCoPE

Sample preparation method: nPOP

## pSCoPE data processed to ASCII text matrices

### Benchmarking experiments: Figure 1b/e data

• 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.

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

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

### Benchmarking experiments: Figure 1c/d data

• 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.

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

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

### Bone-marrow-derived macrophage experiments: Figures 2, 3, and 4

• 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.

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

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

## pSCoPE RAW data and search results from MaxQuant

The Massive repository below contains RAW mass-spectrometry data files generated by a Q exactive instrument as well as the search results from analyzing the RAW files by MaxQuant and by DART-ID. Please consult the linked files for more information on the included files: