Table 9 Parameters setting of MASCOT engine.
Item | Value |
|---|---|
Enzyme | Trypsin |
Max Missed Cleavages | 2 |
Fixed modifications | Carbamidomethyl (C), iTRAQ 8plex (N-term), iTRAQ 8plex (K) |
Variable modifications | Oxidation (M), iTRAQ 8plex (Y) |
Peptide Mass Tolerance | ±20 ppm |
Fragment Mass Tolerance | 0.1 Da |
Database | uniport _Oryza_sativa_168274 _ 20170123.fasta |
Database pattern | Decoy |
Peptide FDR | ≤0.01 |
Protein Quantification | The protein ratios are calculated as the median of only unique peptides of the protein |
Experimental Bias | Normalizes all peptide ratios by the median protein ratio. The median protein ratio should be 1 after the normalization. |
