Table 5.
MaxQuant search library parameter settings.
| Item | Value |
|---|---|
| Type | Reporter ion MS2 |
| Isobaric labels | TMT 6plex |
| Enzyme | Trypsin |
| Reporter mass tolerance | 0.005 Da |
| Max Missed Cleavages | 2 |
| Main search Peptide Tolerance | 4.5 ppm |
| First search Peptide Tolerance | 20 ppm |
| MS/MS Tolerance | 20 ppm |
| Fixed modifications | Carbamidomethyl (C) |
| Variable modifications | Oxidation (M), Acetyl (Protein N-term), |
| Database | Bamboo.fasta |
| Database pattern | Target-Reverse |
| PSM FDRa | ≤0.01 |
| Protein FDR | ≤0.01 |
| Protein quantification | Razor and unique peptides were used for protein quantification. |
aFDR = FP/ (FP + TP), FP (False Protein, from Decoy database) and TP (True Protein, from True database).