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Table 1 SCoPE2 improves quantitative accuracy, depth of proteome coverage, ease of sample preparation, and cost-effectiveness 2–10-fold over SCoPE-MS. Quantitative accuracy is evaluated by comparing relative protein ratios from in silico averaged single cells to bulk data, shown in Fig. 4c. The number of single-cell measurements per hour was estimated considering both filtering levels described in the “Methods” section. The cost of SCoPE-MS does not include the cost of sonication instrumentation. The throughput estimates for SCoPE2 are based on TMT 16-plex

From: Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2

Benchmark SCoPE-MS SCoPE2 Relevant figure
Correlation to benchmark fold changes 0.2 0.89 4c
Purity of ions isolated for quantification 79% 97% 3d
Single-cell protein measurements/h
 - “1% FDR” filtering 610 5213 3f
 - “Stringent” filtering N/A 3417 3f
Sample preparation
 - Time, h/cell < 1 < 0.03 3a
 - Cost, USD/cell < 10 < 1 1a
LC-MS/MS
 - Time, h/cell 0.50 0.12 3a
 - Cost, USD/cell 48–96 10–20 1a
  1. LC-MS/MS cost assumes MS facility fee of $100–200 per hour