Table 1.
Details of the in silico (Disease), in-house built PCa spectral libraries acquired at Orbitrap Fusion Lumos Tribrid (Thermo Scientific, Waltham, MA, USA) mass spectrometer (in micro-flow mode) (Lumos), Sciex TripleTOF 6600 mass spectrometer in micro-flow mode (S-Micro) and nano-flow mode (S-Nano) and combined library (Combined-PCa) built after the integration all four, using an online tool, iSwathX (at protein FDR of 1%). S-Micro was used as base library and others added on in the process of integration.
| Characteristics | Proteotypic | Proteotypic and Shared |
|---|---|---|
| Disease Library | ||
| Proteins | 346 | 346 |
| Peptides | 4503 | 4503 |
| Precursors | 7000 | 7000 |
| Transitions | 41,995 | 41,995 |
| LUMOS library | ||
| Proteins | 561 | 760 |
| Peptides | 9176 | 9577 |
| Precursors | 13,263 | 13,891 |
| Transitions | 79,578 | 83,346 |
| S-Micro Library | ||
| Proteins | 348 | 484 |
| Peptides | 5899 | 6210 |
| Precursors | 7931 | 8360 |
| Transitions | 47,586 | 50,160 |
| S-Nano Library | ||
| Proteins | 508 | 712 |
| Peptides | 4110 | 4478 |
| Precursors | 5596 | 6104 |
| Transitions | 33,576 | 36,624 |
| Combined Prostate Cancer Serum Library | ||
| Proteins | 950 | 1227 |
| Peptides | 13,265 | 13,793 |
| Precursors | 17,758 | 18,479 |
| Transitions | 110,346 | 114,684 |