Settings used for Proteomic Analysis in Skyline-daily

Peptide Settings
	Digestion: Enzyme = Trypsin [KR | P]
		        Max missed cleavages = 2
		        Background proteome = None
	Modifications: Carbamidomethyl (C), Oxidation (M) - variable
			  Max variable mods = 3
			  Max neutral losses = 1
			  Isotop label type = heavy
			  Internal standard type = heavy
	Library: Keep redundant library
		   Cut-off score = 0.95
		   Pick peptides matching Library

Transition Settings
	Predition: Precursor mass = Monoisotopic
		      Product ion mass = Monoisotopic
		      Collision energy = Thermo TSQ Vantage
		      Declustering potential = None 
	Filter: Precursor charges = 2,3,4
	           Ion charges = 1,2,3
	           Ion types = p
	           Product ions: From m/z/ > precursor
	          			To 3 ions
				Always add N-terminal to Proline
	           Auto-select all matching transitions
	Library: Ion match tolerance = 0.5 Th
		   Do not check "If a library spectrum is available, pick its most intense ions"
	Instrument: Min m/z = 50 Th, Max m/z = 2000 Th
		         Method match tolerance m/z = 0.055 Th
	Full-Scan: Isotope peaks included = Count
		       Precursor mass analyzer = Orbitrap
		       Peaks = 3
		       Resolving power = 60,000 at 400 Th
		       Isotope labeling enrichment = Default
		       Acquisition method = None
		       Use only scans within 5 minutes of MS/MS IDs