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

Data

• 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.

• Peptides x Samples
  • Proteins x single cells at 1% FDR, imputed and batch corrected.

• 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.

• Source data for figures

  • Figure 2: LC-MS/MS setup for SCoPE2 experiments

  • Figure 3: Evaluating data acquisition and interpretation using DO-MS diagnostic plots

  • Figure 4: Principal Component Analysis of results from SCoPE2 analysis

  • Extended Data Figure 1: The ABIRD device may suppress contaminant ions

Workshops

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.

• Design of single-cell proteomics experiments using SCoPE2
• Sample preparation for single-cell MS analysis by SCoPE2
• High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity