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. Author manuscript; available in PMC: 2018 Jul 24.
Published in final edited form as: Nat Protoc. 2017 Jul 27;12(8):1683–1701. doi: 10.1038/nprot.2017.054

Parameter Value

Variable modification Fixed modification Oxidation (M) Acetyl (Protein N-term) Deamidation PyroGlu (Q) Carbamidomethyl (C) iTRAQ or TMT-10
Maximum missed cleavages 4
Maximum charge 5
Precursor mass tolerance (p.p.m.) 20
Product mass tolerance (p.p.m.) 20
Peptide FDR 0.01
Protein FDR 0