Table II. 6× GPF-DIA acquisition settings for DIA-only library generation with Thermo instruments.

	QE	QE+	QE-HF	QE-HFX	Fusion	Lumos
Est. Scan Rate	10 Hz	10 Hz	10 Hz	10 Hz	10 Hz	10 Hz
MS1 Scans
Range	395–505 m/z, 495–605 m/z, etc…	395–505 m/z, 495–605 m/z, etc…	395–505 m/z, 495–605 m/z, etc…	395–505 m/z, 495–605 m/z, etc…	395–505 m/z, 495–605 m/z, etc…	395–505 m/z, 495–605 m/z, etc…
Resolution	35000	35000	60000	60000	60000 (Orbi)	60000 (Orbi)
Max IIT (ms)	60	60	60	60	60	60
AGC Target	1E+6	1E+6	1E+6	1E+6	4E+5	4E+5
Data Type	Centroid	Centroid	Centroid	Centroid	Centroid	Centroid
MS2 Scans
Windowing Scheme	6x GPF-DIA w/4 m/z staggered	6x GPF-DIA w/4 m/z staggered	6x GPF-DIA w/4 m/z staggered	6x GPF-DIA w/4 m/z staggered	6x GPF-DIA w/4 m/z staggered	6x GPF-DIA w/4 m/z staggered
Resolution	17500	17500	30000	30000	30000 (Orbi)	30000 (Orbi)
Max IIT (ms)	60	60	60	60	60	60
AGC Target	1e6	1e6	1e6	1e6	4e5	4e5
Loop Count	25	25	25	25	25	25
Default Charge	3	3	3	3	3	3
(N)CE	27	27	27	27	33 (HCD)	33 (HCD)
Data Type	Centroid	Centroid	Centroid	Centroid	Centroid	Centroid