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. Author manuscript; available in PMC: 2016 Jan 25.
Published in final edited form as: Nat Protoc. 2013 Sep 19;8(10):1950–1960. doi: 10.1038/nprot.2013.120
MS Method Parameter Value
Polarity positive
Full MS
Microscans 1
Resolution 70,000
AGC Target 3 × 106 ion counts
Maximum Ion Time 10 ms
Scan Range 300-1800 m/z
dd-MS2
Microscans 1
AGC Target 5 × 104 ion counts
Maximum Ion Time 120 ms
Loop Count 12
Isolation Window 2.5 m/z
Fixed First Mass 100 m/z
Normalized Collision Energy 25
dd Settings
Underfill Ratio 5%
Charge Exclusion unassigned, 1, ≥7
Peptide Match on
Exclude Isotopes on
Dynamic Exclusion 20 s