Table 1. Parameters for Mascot, SEQUEST, and MaxQuant Andromeda.

Parameter	Setting
Database	Human SwisProt (Downloaded May 1, 2012)
Missed cleavages	2
Enzyme specificity	Typsin
Precursor mass tolerance	20 ppm
Fragment mass tolerance	0.8 Da
Dynamic modifications	Deamidated (NQ), Oxidation (M), Acetylation (N-term)
Static modifications	Propionamide (C)
Protein False Discovery Rate	1%