Table 9.
Settings for the generation of the spectral library in Spectronaut
| Pulsar search | ||
| Peptides | Enzymes/Cleavage Rules | Trypsin/P |
| Digest Type | Specific | |
| Missed Cleavages | 4 | |
| Modifications | Max Variable Modifications | 5 |
| Fixed Modifications | Carbamidomethyl (C) | |
| Variable Modifications | Acetyl (Protein N-term) Oxidation (M) Malonyl (K) |
|
| MS2 | Ion Types | b; y |
| Library generation | ||
| Tolerances | Thermo Orbitrap | |
| Calibration Search | Dynamic | |
| MS1 Correction Factor | 1 | |
| MS2 Correction Factor | 1 | |
| Main Search | Dynamic | |
| MS1 Correction Factor | 1 | |
| MS2 Correction Factor | 1 | |
| Identification | Pulsar | |
| PSM FDR | 0.01 | |
| Peptide FDR | 0.01 | |
| Protein FDR | 0.01 | |
| PTM Localization Filter | None | |
| Spectral Library Filters | Fragment Ions | |
| Ion AA Length (min) | N = 3 | |
| m/z | 200 - 3,000 | |
| Relative Intensity | Min = 5 | |
| Precursors | ||
| Best N Fragments per Peptide | 3–6 | |
| Modifications | None | |