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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
Parameter Value
Variable modification Oxidation (M)
Acetyl (Protein N-term)
GlyGly (K)
Fixed modification Carbamidomethyl (C)
Maximum missed cleavages 2
Maximum charge 6
First search ppm 20
Main search ppm 6
MS/MS tolerance (ppm) 20
Peptide FDR 0.01
Site FDR 0.01
Protein FDR 0.01
Minimum peptide length 6