Molecular data show less variability than protein spectra, but are more time-consuming and cost-intensive. On the contrary, mass spectra are able to discriminate between some developmental stages. As a result, we suggest the application of species typing based on proteomic fingerprinting as an alternative approach for a rapid and cost-effective method. Once an accessible reference library for metazoan proteome fingerprints is established and by working with adequate software, species can be identified straightforwardly within minutes. We suggest that this method is especially useful for analysing a high number of samples or when specimens are difficult to determine/discriminate with respect to congeners or life history stages.
So far the authors of a new study which compares DNA-based identification methods (e.g. DNA Barcoding) with proteome fingerprints generated through so called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-Tof-MS). This technology has had a major impact in many fields of the life sciences over the last two decades. Samples (cells, molecules, peptides or proteins) co-crystallize with a matrix solution on a target plate. A pulsed laser causes desorption of the sample mixture, followed by the ionization of the sample. In a strong electric field, the ions are accelerated along a vacuum tube. Based on the time of flight, the different masses of the single molecules are represented as spectra.
MALDI-Tof-MS studies for rapid species identification were e.g conducted using species-specific proteome profiles of fish, flies, and copepods. It has been argued that for a rapid identification of individuals, techniques based on nucleotide sequences still have the disadvantage of requiring a number of steps, i.e. DNA extraction, polymerase chain reaction, gel electrophoresis, and are therefore considered more costly and time-consuming.
As other methods that are proposed for rapid species identification MALDI-Tof-MS could be complementary to what we already have in place. While methods based on molecular biology generally demand some a priori knowledge of the sample under investigation (e.g. for primer selection) and, more importantly, can be slow and laborious with results that may depend on experimental variables, a mass spectral approach can be much more straightforward, requiring minimal time and relatively low costs. However, a prerequisite is the creation of a taxonomically comprehensive molecular profile database for known species. That reminds me of something...