Table I. Mass spectrometry metrics and methodology by center.
| Resolution | iTRAQ | Label-Free |
|||
|---|---|---|---|---|---|
| High | Low | ||||
| Center | A | B | C | D | E |
| Instrument | Q-Exactive | Orbitrap Velos | Orbitrap Velos | Q-Exactive | Orbitrap Velos |
| Fractions | 25 | 25 | 24 | 24 | 15 |
| Replicates | 7 | 6 | 5 | 2 | 28 |
| Gradient (min) | 110 | 90 | 100 | 240 | 80 |
| Total peptides | 143,790 | 75,440 | 81,888 | 49,351 | 38,437 |
| SNV peptides | 642 | 267 | 274 | 79 | 72 |
Proteome analysis of basal and luminal PDX tumors was completed across five centers (A-E) using Thermo Fisher Q-Exactive or Orbitrap Velos instrumentation. The number of fractions, LC-MS/MS gradient length, MS/MS model, number of PDX sample process replicates, and the average number unique total, single nucleotide variant (SNV) and novel junction (NSJ) peptides are given for each center. All five centers used bRPLC for LC-MS/MS separation.