Article: Huffman et al, 2022, version 2

Single-cell proteomics method: pSCoPE

Sample preparation method: nPOP

Model systems: Primary murine bone-marrow-derived macrophages, as well as HEK293 and melanoma cell lines.

 

 

Processed pSCoPE Data RAW pSCoPE Data

 

pSCoPE data processed to ASCII text matrices

Benchmarking experiments: Figure 2a data, pSCoPE acquisition

  • 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.

 

 

  • 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 2b/c/d/e data, pSCoPE acquisition

  • 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.

 

 

  • 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 2a/b/c/d data, Shotgun acquisition

  • 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.

 

 

  • 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 4, 5, and 6

  • 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.

 

 

  • 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.

 

 

 

Files needed to regenerate preprint figures

 

 

 

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: