A method to compare MALDI-TOF MS PMF spectra and its application in phyloproteomics

Abstract

The suitability of a proteomic approach was explored to establish phylogenetic relationships among closely-related species. Decapoda penaeid shrimps were chosen as case study because these species have been widely studied and their phylogenetic relationships have been inferred by extensively validated methods, among which mitochondrial DNA-based PCR studies have provided relevant information Thus, MALDI-TOF mass spectrometry (MS) peptide mass fingerprinting (PMF) of arginine kinase was performed, this enzyme being selected from the sarcoplasmic proteome of such species due to the interspecific variability of their pI values. The presence or absence of selected peptides in the MS spectra was used as a molecular marker for phylogenetic analysis. Based on the cluster analysis of the MALDI-TOF PMF spectra obtained, a dendrogram was generated which could be validated with those obtained using DNA-based methods. © 2009 Springer Berlin Heidelberg.