Article: Huffman et al, 2022, version 2
- The data from version 1 are available at Huffman et al, 2022, version 1
- Peer reviewed article: Huffman RG, Leduc A, Wichmann C, … and Slavov N, Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. Nat Methods, doi: 10.1038/s41592-023-01830-1 (2023)
- Research Briefing: Extending the sensitivity, consistency and depth of single-cell proteomics, OA
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
Metadata and data processed to ASCII text matrices
Benchmarking experiments: Figure 2a data, pSCoPE acquisition
- Metadata: Cells.csv
Annotationxsingle 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.
- Peptides-raw.csv
Peptidesxsingle cellsat 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
Proteinsxsingle cellsat 1% FDR, imputed and batch corrected.
Benchmarking experiments: Figure 2b/c/d/e data, pSCoPE acquisition
- Metadata: Cells.csv
Annotationxsingle 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.
- Peptides-raw.csv
Peptidesxsingle cellsat 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
Proteinsxsingle cellsat 1% FDR, imputed and batch corrected.
Benchmarking experiments: Figure 2a/b/c/d data, Shotgun acquisition
- Metadata: Cells.csv
Annotationxsingle 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.
- Peptides-raw.csv
Peptidesxsingle cellsat 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
Proteinsxsingle cellsat 1% FDR, imputed and batch corrected.
Bone-marrow-derived macrophage experiments: Figures 4, 5, and 6
- Metadata: Cells.csv
Annotationxsingle 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.
- Peptides-raw.csv
Peptidesxsingle cellsat 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
Proteinsxsingle cellsat 1% FDR, imputed and batch corrected.
Files needed to regenerate preprint figures
- Additional data files necessary for generating figures from the pSCoPE preprint.
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:
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MassIVE Repository: