Table II Comparison of trypsin-based digestion protocols after analysis by standard qualitative nanoLC-MS/MS
Digestion protocolPeptide identificationsProtein identifications
Rep 1Rep 2Rep 3SumaAverage pIAverage GRAVYRep 1Rep 2Rep 3SumaAverage MW (kDa)aAverage coveragebPeptides/protein
ISD:RG22252241214829886.31−0.2840441436745541.618.76.6
ISD:Urea23342319238731536.35−0.2337236636142143.621.67.5
ISD:SDC19582515276233596.30−0.2134538741144442.321.37.6
SF-ISD:SDC26822536275034896.33−0.2242040743048443.420.87.2
SF-ISD:SDS-Urea/-15891642195223486.13−0.3539742638146844.013.55.0
SF-ISD:SDS/SDC944112477012486.11−0.2925227020629043.212.74.3
SF-ISD:SDS/-154149482085.57−0.45106984212150.44.51.7
  • a Identified proteins and reported molecular weights represent mature protein forms as non-mature sequences such as signal peptides and mitochondrial transit sequences have been removed, as described in Material and Methods.

  • b Values represent the sum of unique peptide sequences and protein identifications from triplicate experiments.