• Use Ion Source Settings from Tune = False
• Method Duration (min)= 120
• Ion Source Type = NSI
• Spray Voltage: Positive Ion (V) = 2000
• Spray Voltage: Negative Ion (V) = 600
• Sweep Gas (Arb) = 0
• Ion Transfer Tube Temp (°C) = 275
• APPI Lamp = Not in use
• Pressure Mode = Standard
• Default Charge State = 1

• Start Time (min) = 0
• End Time (min) = 120
• Cycle Time (sec) = 2

Scan MasterScan

• MSn Level = 1
• Use Wide Quad Isolation = True
• Detector Type = Orbitrap
• Orbitrap Resolution = 60K
• Mass Range = Normal
• Scan Range (m/z) = 300-1350
• Maximum Injection Time (ms) = 50
• AGC Target = 2000000
• Microscans = 1
• RF Lens (%) = 30
• Use ETD Internal Calibration = False
• DataType = Profile
• Polarity = Positive
• Source Fragmentation = False
• Scan Description =

Filter MIPS

• MIPS Mode = Peptide

Filter ChargeState

• Include undetermined charge states = False
• Include charge state(s) = 2-6
• Include charge states 25 and higher = False

Filter Dynamic Exclusion

• Exclude after n times = 1
• Exclusion duration (s) = 5
• Mass Tolerance = ppm
• Mass tolerance low = 10
• Mass tolerance high = 10
• Exclude isotopes = True
• Perform dependent scan on single charge state per precursor only = False

Data Dependent Properties

• Data Dependent Mode= Cycle Time

• Scan ddMSnScan
• MSn Level = 2
• Isolation Mode = Quadrupole
• Isolation Window = 0.7
• Use Isolation m/z Offset = False
• Multi-notch Isolation = False
• Scan Range Mode = Define m/z range
• Scan Priority= 1
• ActivationType = HCD
• Is Stepped Collision Energy On = False
• Stepped Collision Energy (%) = 5
• Collision Energy (%) = 30
• Is EThcD Active = False
• Detector Type = IonTrap
• Ion Trap Scan Rate = Turbo
• Scan Range (m/z) = 200-1200
• Maximum Injection Time (ms) = 15
• AGC Target = 40000
• Inject ions for all available parallelizable time = False
• Microscans = 1
• Use ETD Internal Calibration = False
• DataType = Centroid
• Polarity = Positive
• Source Fragmentation = False
• Scan Description =