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