Table 10.

Settings for inspecting the data in Skyline

Peptide settings
Digestion	Enzymes	Trypsin [KR|P]
	Max missed cleavages	4
Filters	Min length	5
	Max length	35
	Auto-select all matching peptides	True
Library	Pick peptides matching	Library
Modifications	Structural modifications	Carbamidomethyl (C, fixed) Acetyl (N-term, variable) Oxidation (M, variable) Malonyl (K, variable)
	Max variable mods	3
Transition settings
Filter	Precursor charges	2, 3, 4
	Ion charges	1, 2, 3
	Ion types	p, y, b
	Product ions
	From	ion 2
	To	last ion
	Auto-select all matching transitions	True
Library	Ion match tolerance	0.5 m/z
	If a library spectrum is available, pick its most intense ions	True
	Pick	10 product ions
	From filtered ion charges and types	True
Instrument	Min m/z	200
	Max m/z	1500
	Method match tolerance m/z	0.055 m/z
Full-scan	MS1 filtering
	Isotope peaks included	Count
	Precursor mass analyzer	Orbitrap
	Peaks	3
	Resolving power	120,000 at 200 m/z
	MS/MS filtering
	Acquisition method	DIA
	Product mass analyzer	Orbitrap
	Isolation scheme	cf. Step 27
	Resolving power	30,000 m/z at 200 m/z
	Retention time filtering
	Include all matching scans	True