Article: Petelski et al, 2021

Peer reviewed article: Petelski, A.A., Emmott, E., Leduc, A. et al. Multiplexed single-cell proteomics using SCoPE2. Nat Protoc 16, 5398–5425 (2021). 10.1038/s41596-021-00616-z , Protocol Website

Single-cell proteomics method: SCoPE2

Sample preparation method: mPOP

Model systems: Cell lines of monocytes (U937 cells) and Hela cells.


Protocol data Recorded workshops



  • RAW Files

  • Peptides x Samples

    • 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.



  • Cells.txt
    • 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.



The presentations below describe sample preparation and data analysis for the latest version of Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), SCoPE2. They were presented at the workshop of the second Single Cell Proteomics Conference.