MALDI-TOF MS profiling approach: how much can we get from it?

Mass spectrometry has brought unprecedented possibilities in the field of proteomics. The advances obtained in the last 10 years have been outstanding and have enabled faster and more reliable data acquisition and comparison. One powerful method developed was the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) approach, primarily used for the rapid and accurate identification of microorganism species. At least three commercial manufacturers developed systems (instrument, processing method, and databases) for this purpose with relatively similar results although not completely comparable or exchangeable. These methods were conceived for species level identification; however we explored these approaches with some few modifications for expression profiling purposes. We tested different samples, from diverse organisms (not only microorganisms) and found that MALDI-TOF MS profiling methods also have the ability to differentiate samples submitted to different biological conditions (e.g., biotic or abiotic stresses). In the case of MALDI-TOF MS profiling traditional approach, the extraction procedure is based on the enrichment of ribosomal proteins. By using different extraction protocols, samples can also be enriched with different types of proteins. Indeed, when proteins considered for profiling were further analyzed byMALDI TOF/TOFmethods, other proteins could also be detected. Although MALDI-TOF MS profiling methods have been used in several tissues and samples, this approach has been rarely employed in plants. One of the applications in plant research is the identification of biomarkers associated to disease, which could, for example, help on quarantine procedures. Overall, MALDI-TOF MS profiling has a high potential to contribute for sample differentiation and biomarker identification and should be better explored in plant proteomics.