Table 2.
A summary of the filtration steps applied to the SCoPE2 data and the number of experiments, single cells, unique peptides, and unique proteins remaining in the dataset after each filtering step
| Runs | Single cells | Proteins | Peptides | |
|---|---|---|---|---|
| Number of runs | 179 | |||
| Remove runs with less than 500 PSMs | 173 | |||
| Filter to peptide and protein FDR < 1% | 173 | 1660 | 6138 | 25,015 |
| Remove reverse and contaminant hits | 173 | 1660 | 6083 | 24,743 |
| “FDR = 1%” filtering (Fig. 3f) | 173 | 1660 | 6083 | 24,743 |
| Remove peptide with MS2 purity (PIF) below 0.8 | 173 | 1660 | 5271 | 16,173 |
| Remove peptides with abnormally high intensity | 173 | 1660 | 4788 | 14,084 |
| Remove cells with median CV below 0.365 | 172 | 1490 | 4735 | 13,809 |
| Remove proteins quantified in less than 15 cells | 172 | 1490 | 3042 | 8304 |
| “Stringent” filtering (Fig. 3f) | 172 | 1490 | 3042 | 8304 |