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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