Heramb M. Kulkarni¹, V. Ramesh², R. Srinivas² and M.V. Jagannadham¹

¹Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad-500 007, India. ²Indian Institute of Chemical Technology, Hyderabad-500 007, India.

Abstract

Several approaches have been described to identify proteins from MALDI MS/MS mass spectra. The sequence of tryptic peptides is determined by database searching or by de novo sequencing. Different algorithms are available to determine peptide sequence using mass spectra. False discovery of peptides is an associated problem with it. A combination of chemical modifications followed by mass spectral analysis helps in overcoming this problem. Acetylating the tryptic peptides of β-galactosidase in methanol is found to increase the b-ion signal intensity in MALDI TOF mass spectrometry. The method of acetylation is extended to the tryptic peptides of the proteins of an Antarctic bacterium Pseudomonas syringae, whose genome sequence is not known. These proteins are identified by searching the available database of the Pseudomonas spp at NCBI using the MS/MS spectra. The sequences of the peptides are validated using the CID mass spectra of the acetylated tryptic peptides.