The detection of proteins profiles associated with disease states dates back to the very beginning of proteomics, when two-dimensional gel electrophoresis was first applied to clinical material. The advent of novel mass spectrometers enable to resolve thousands of protein and peptide species in body fluids is set to revolutionize protein-based diagnostic. In fact, mass spectrometry has increasingly become the method of choice for analysis of complex protein samples establishing itself as an indispensable technology to interpret the information encoded in genomes. This new era started with the discovery and development of protein ionization methods, as recognised by the 2002 Nobel prize in chemistry [4]. The ability of mass spectrometry to identify and accurately quantify even small amount of a specific protein from increasingly complex mixtures is becoming a primary driving force in proteomics. The rapid development of this technology has carried out instrument with an increased sensitivity, robustness and data handling with improved analytical performance.
Direct mass spectrometry approach of complex mixtures, is today, the last challenge for gel-free analysis of disease biomarkers. In particular, Linear Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF-MS), is a promising technique for clinical applications given its high sensitivity, accuracy and resolution in discriminating the low molecular weight protein profiles [5, 6]. Quantitative data are achievable by the use of internal standard gaining precision and accuracy within 20-25% . Moreover time and cost of analysis for each sample are particularly low, given the ion source set up, which eventually might handle hundreds of samples in a single acquisition batch. These qualities have made MALDI-TOF-MS as an instrument of choice to investigate large number of clinical relevant molecules in serum, blood, urine, tissue extracts and whole cells [7, 8]. Linear MALDI-TOF-MS coupled to surface activated sample targets (SELDI-TOF-MS) has already been recently employed by several groups to detect potential novel biomarkers in different biological samples [9-11]. Approaches include comparative analysis of protein expression in normal and disease samples to identify aberrantly expressed proteins that may represent new disease-markers. Serum patterns that distinguish between disease and normal subject with remarkable accuracy have been reported for several type of cancers and other diseases [12]. This direct mass spectrometry approach yield to a comprehensive profiles of peptides and proteins in biological fluids without the need to first carry out proteins separations and requiring reduced amount of sample for high throughput. Researchers are employed to develop new and automated peptide extractions, crystallizations, spectral acquisition and signal processing. Computational methodologies and bioinformatics tools are also necessary to develop models to analyze and compare large numbers of data points, essential for valuable and significant data mining (Fig. 1).
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