Discrimination of different species from the genus Drosophila by intact protein profiling using matrix-assisted laser desorption ionization mass spectrometry

<p>Abstract</p> <p>Background</p> <p>The use of molecular biology-based methods for species identification and establishing phylogenetic relationships has supplanted traditional methods relying on morphological characteristics. While PCR-based methods are now the commonly accepted gold standards for these types of analysis, relatively high costs, time-consuming assay development or the need for <it>a priori </it>information about species-specific sequences constitute major limitations. In the present study, we explored the possibility to differentiate between 13 different species from the genus <it>Drosophila </it>via a molecular proteomic approach.</p> <p>Results</p> <p>After establishing a simple protein extraction procedure and performing matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) with intact proteins and peptides, we could show that most of the species investigated reproducibly yielded mass spectra that were adequate for species classification. Furthermore, a dendrogram generated by cluster analysis of total protein patterns agrees reasonably well with established phylogenetic relationships.</p> <p>Conclusion</p> <p>Considering the intra- and interspecies similarities and differences between spectra obtained for specimens of closely related <it>Drosophila </it>species, we estimate that species typing of insects and possibly other multicellular organisms by intact protein profiling (IPP) can be established successfully for species that diverged from a common ancestor about 3 million years ago.</p