Table 2.

The filtering of proteins from endogenous tryptic peptides (TRYP) or tryptic phospho peptides (STYP) from the stepwise extraction of human EDTA plasma with a mixture of organic solvent and water where MS/MS correlations from precursor ions of greater than ~ E4 (10,000) arbitrary counts were accepted from 1508 LC–ESI–MS/MS runs

MS/MS spectra	15,968,550
Protein filtering
Protein library	157,478
Correlations	94,483,230
Best charge state (Filter 1)
Protein accessions	156,280
Correlations	19,889,758
Best charge state and peptide sequence (Filter 2)
Protein accessions	156,279
Correlations	19,197,152
Rank 1 Peptides
Peptide identification count	19,197,152
Distinct peptide identification count	4,631,474
Distinct peptide sequence count	1,916,672
Peptides from ≥ 3 correlations per protein	486,895

About 12% of MS/MS spectra from precursors greater than E4 counts were accepted as the best fit to a fully tryptic peptide or phosphopeptide