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. Author manuscript; available in PMC: 2020 May 1.
Published in final edited form as: Nat Protoc. 2019 Dec 20;15(1):161–180. doi: 10.1038/s41596-019-0260-5
Spectrum Files RC Dynamic modification: phosphorylation on serine, threonine or tyrosine. Deamidation of asparagine residues. Static modification: carbamidomethylation (C).
Spectrum Selector Default
PMI-Byonic Maximum number of missed cleavages: 2
Precursor mass tolerance: 10 p.p.m.
Fragment mass tolerance: 0.6 Da
Modifications: carbamidomethylation (C), oxidation (M), acetyl protein N-term, deamidation (N) or phosphorylation (S, T, Y).