Table 1.
Key Configuration Parameters for MyriMatch, Sequest, DirecTag, and InsPecTa
| precursor/fragment analyzer | LTQ/LTQ | FTMS/LTQ | Orbi/LTQ | Orbi/Orbi | Quad/TOF | TOF/TOF |
|---|---|---|---|---|---|---|
| Precursor m/z tolerance | 1.25 | 0.1 | 0.1 | 0.1 | 0.25 | 0.25 |
| Fragment m/z tolerance | 0.5 | 0.5 | 0.5 | 0.1 | 0.25 | 0.25 |
| Precursor mass type | avg | mono | mono | mono | mono | mono |
| Precursor isotope adjust | none | ± neutron | ± neutron | ± neutron | ± neutron | ± neutron |
| InsPecT mode | ESI-ION-TRAP | FT-Hybrid | FT-Hybrid | QTOF | QTOF | QTOF |
a
These settings reflect the different mass accuracies of the various data sets employed in this manuscript. InsPecT did not have a mode ideal for the Orbi/Orbi data, and so its QTOF mode was employed for this set. MyriMatch was allowed to adjust precursor mass by one neutron in isotopically resolved MS scans; Sequest did not perform these adjustments. Exhaustive configuration details are available in Supporting Information.