Table 2.
Parameters for proteome discoverer searches
| LC parameters | DDA | MS2-MS3 | EthcD |
|---|---|---|---|
| Database | Sequence-specific SwissProt | Generated from DDA experiment | Generated from DDA experiment |
| Precursor selection | Use MS1 precursor | Use MS (n-1) with parent precursor | Use MS (n-1) parent precursor |
| Acquisition strategy | Not applicable | MS2_MS3 | MS2_MS2 |
| Mass tolerance MS1 | 10 ppm | 10 ppm | 10 ppm |
| Mass tolerance MS1 | 0.5 Da (ITMS) | 20 ppm (FTMS) 0.5 Da (ITMS) |
20 ppm (FTMS) |
| Dynamic modifications | Oxidation (M) DSSO modification (K, 158.004 Da) Acetylation (Protein N-term) |
Oxidation (M) DSSO modification (K, 158.004 Da) Acetylation (Protein N-term) |
Oxidation (M) DSSO modification (K, 158.004 Da) Acetylation (Protein N-term) |
| Peptide FDR (Percolator) | 0.01 | – | – |
| Peptide FDR (Xlinkx Validator) | – | 0.01 | 0.01 |
| Additional criteria for identification | Two peptides per protein | High quality MS/MS spectra identified for 3 out of the 4 DSSO (alkene and thiol) peptides | Able to identify sequence specific ions consistent with both cross-linked peptides in the spectrum. |