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