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. Author manuscript; available in PMC: 2018 Nov 1.
Published in final edited form as: Nat Protoc. 2018 Jul;13(7):1632–1661. doi: 10.1038/s41596-018-0006-9
Parameter Value
Variable modification Oxidation (M)
Acetyl (protein N-term)
Deamidation (N)
PyroGlu (Q)
Fixed modification Carbamidomethyl (C)
TMT-10 (peptide N-term, K)
Digest Trypsin Allow P
Maximum missed cleavages 4
Maximum charge 5
Precursor mass tolerance (p.p.m.) 20
Product mass tolerance (p.p.m.) 20
Peptide FDR (%) 1
Protein FDR (%) 0