Table III. PeptideAtlas coverage of published protein lists. Percentages in column B are relative to numbers in column A.
| Plasma protein identification list | Total proteins | (A) In PeptideAtlas combined protein sequence databasea | (B) In Human Plasma PeptideAtlas exhaustive set (of those in column A) | |
|---|---|---|---|---|
| Hortin et al. highly abundant plasma proteins (48) | 150 | 126 | 126 | 100% |
| Kuzyk et al. moderate/high concentration plasma proteins reproducibly detectable by LC-MRM/MS analysis of whole tryptic digests; nearly all reported as potential disease markers (56) | 45 | 45 | 45 | 100% |
| Carrascal et al. LC-MS/MS derived plasma phosphoproteins with peptide identified by >1 search engine (55) | 44 | 44 | 43b | 98% |
| Schenk, et al. LC-MS/MS derived plasma proteins (non-immunoglobulin) (16) | 697 | 554 | 503 | 91% |
| Polanski and Anderson potential cancer biomarkers (57) | 1261 | 1054 | 326 | 31% |
a Swiss-Prot 2010–04 + IPI v3.71 + Ensembl v54.37.
b A single spectrum for the missing phosphoprotein was identified by our computational pipeline, but discarded during our manual validation process.