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Table 1 The parameters Proteome of Discoverer 1.4

From: Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

Item value
Enzyme Trypsin
Max Missed Cleavages 2
Fixed modifications Carbamidomethyl (C), iTRAQ4/8plex (N-term), iTRAQ 4/8plex (K)
Variable modifications Oxidation (M), iTRAQ 4/8plex (Y)
Peptide Mass Tolerance ± 20 ppm
Fragment Mass Tolerance 0.1 Da
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.