Article: Huffman et al, 2022, version 1
- The data from version 2 are available at Huffman et al, 2022, version 2
Single-cell proteomics method: pSCoPE
Sample preparation method: nPOP
Model systems: Primary murine bone marrow derived macrophages and a pancreatic ductal adenocarcinoma (PDAC) cell line.
Processed pSCoPE Data RAW pSCoPE Data
pSCoPE data processed to ASCII text matrices
Benchmarking experiments: Figure 1b/e data
- Peptides-raw.csv
Peptides
xsingle 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
xsingle cells
at 1% FDR, imputed and batch corrected.
- Cells.csv
Annotation
xsingle 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
xsingle 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
xsingle cells
at 1% FDR, imputed and batch corrected.
- Cells.csv
Annotation
xsingle 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
xsingle 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
xsingle cells
at 1% FDR, imputed and batch corrected.
- Cells.csv
Annotation
xsingle 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
- 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: