An improved clean sonoreactor-based method for protein identification by mass spectrometry-based techniques

A new clean fast (8 min) method for in-solution protein digestion without detergent or urea for protein identification by peptide mass fingerprint and mass spectrometry-based techniques is proposed. The new method avoids the use of time consuming desalting procedures entailing the following four steps done under the effect of an ultrasonic field provided by a sonoreactor: denaturation (1 min) in a mixed solution of water:acetonitrile 1/1 (v/v); protein reduction (1 min); protein alkylation (1 min); and protein digestion (5 min). Five proteins with masses comprised between 14.4 kDa and 97 kDa and the protein split-soret cytochrome c from D. desulfuricans ATCC27774, were successfully identified with this procedure. No differences were found in the sequence coverage or in the number of peptides matched when the new clean method was compared to another one using urea. Twofold better signal-to-noise ratios were obtained in the MALDI spectra from protein samples prepared with the new method when comparing it with a method using urea. The new digestion method avoids the need to remove salt content and increases throughput (six samples at once) while reducing sample loss and contamination from sample handling. © 2008 Elsevier B.V. All rights reserved.