Table 1. Overview of Requirements and Typical Results for Standard Proteomics Protocols, Single-Cell and Minimal Input Protocolsa.
| number of cells prepared (approx. amount of protein prepared) | approximate number of proteins identified (single-shot) | correlation with standard input sample (ρ) | correlation between replicates (ρ) | correlation between RNA abundance (ρ) | |
|---|---|---|---|---|---|
| standard | ∼106–8 (∼5–500 μg) | 2700 | 0.99 | 0.43 | |
| MiProt6 | n/a (25 μg) | 10 000b | 0.60 | 0.38 | |
| in-StageTip7 | n/a (20 μg) | 1435 | 0.97 | ||
| Myers et al.8 | n/a (2 μg) | 5100b | 0.90 | 0.25–0.50 | |
| Wang et al.9 | 5000 (∼500 ng) | 140 | |||
| Wang et al.10 | 500–5000 (∼50–500 ng) | 105–665 | |||
| SP311 | 1000 (n/a) | 1250 | 0.84–0.91 | ||
| NanoPOTS3 | 1–6 (0.2–1.2 ng) | 669–1153c | 0.95–0.97 | ||
| SCoPe-MS5 | 1 (n/a) | 900 | 0.62 | 0.2–0.4 | 0.25 |
| minimal input protocol | 1000 (∼200 ng) | 2500 | 0.81 | 0.99 | 0.39 |
a
Information on input amount, number of detected proteins, and correlations are taken from the original publications. Note that some preparations, e.g., the standard input protocol, do not use all of the prepared material for a single injection into the mass spectrometer. ρ—Spearman correlation coefficient.
b
Fractionated.
c
Using the MaxQuant match between runs algorithm.