Method parameter	Value
Polarity	Positive
Full MS
Microscans	1
Resolution	70,000
Automatic gain control (AGC) target	3 × 106 ion counts
Maximum ion time	5 ms
Scan range	300–1,800 m/z
Data-dependent MS2 (dd-MS2)
Microscans	1
Resolution	17,500 (iTRAQ, TMT- 6); 35,000 (TMT-10)
AGC target	5 × 104 ion counts
Maximum ion time	120 ms
Loop count	12
Isolation window	1.6 m/z
Isolation offset	0.3 m/z
Fixed first mass	100 m/z
Normalized collision energy	27 (iTRAQ), 29 (TMT)
Data-dependent (dd) settings
Underfill ratio	5%
Charge exclusion	Unassigned, 1, 7
Peptide match	Preferred
Exclude isotopes	On
Dynamic exclusion	20 s