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 |