**11. Conclusions**

and treatments tailored to genetic, environmental, and lifestyle factors of individuals will be developed. Showing a great ability in providing reference data for the identification of groups of individuals who share various attributes, these approaches have opened new opportunities for the discovery of potential diagnostic/prognostic protein biomarkers in several pulmonary disorders. By helping researchers in understanding the pathogenesis of respiratory diseases and improve patient care, the recent findings have indeed progressively increased the interest for the application of proteomics in clinical practice. The current chapter was designed to keep the reader informed about the present status of pulmonary proteome. Taken together, the results documented here demonstrate that, after a decade of activity, proteomics of pulmonary diseases is catching up with its promise. The constantly growing number of reports in this area supports the view of this approach as one of the decisive methodological tools for the identification/characterization of disease-associated proteins. In terms of experimental procedures, the basic options available for proteomic investigations consist in the identification of proteins through the use of gel-based or gel-free techniques followed by MS. Undoubtedly, the striking improvement in technologies related to accuracy, when coupled to quantitative approaches, has a great impact on the quality of the results. Obviously, the question arises of whether sophisticated technologies (such as the non-gelbased proteomic procedures) may actually be more fruitful, in terms of candidate protein marker identification, than "conventional" (read electrokinetic) approaches. In light of the versatility and high degree of reproducibility shown by these new potent strategies, a positive answer is perhaps not surprising, at least for one reason. The very high number of peptides identified and quantified results in a higher accuracy, which translates into improved alignment and quantification across spectra. Nevertheless, as documented in this chapter, despite being less sophisticated than competing ones, gel-based techniques still represent a widely used procedure able to generate a reliable protein "fingerprint." Though it may seem nonsense, it is precisely the "limited" amount of information produced by electrokinetic approaches that may result in an easy interpretation of data. The possibility to compare a sample in physiological and pathological conditions allows, in fact, immediate detection of possible relevant changes in protein expression which differentiate the two conditions. These changes are essential in demonstrating progression from health to disease and understanding the relationship between function and modification. The wide spectrum of examples presented in this chapter confirms that the application of 1-DE/2-DE/2-DIGE/CE (followed by MS) to a variety of biological fluids from individuals with different respiratory diseases may result in the production of data with clinical relevance which allow a better understanding of the molecular basis of the disorder investigated. However, as it can be observed from the data presented in this chapter, while peculiar proteins are pointed out as potential biomarkers of specific disorders, a good number of proteins is implicated across a variety of different diseases. This makes the notion of a single biomarker to indicate a specific disease more difficult. For example, while α2-macroglobulin and surfactant protein A have been indicated as candidate biomarkers of both lung fibrosis associated with systemic sclerosis and asthma [27, 37], the former protein (together with other proteins) was suggested to be also a potential biomarker of pulmonary embolism [52]. Indeed, for greater confidence in disease diagnosis or prognosis, a suite of biomarkers would provide more specificity than a single one. In other words, should the identification of hundreds of candidate biomarkers come at the

36 Electrophoresis - Life Sciences Practical Applications

Aside from the interest in deciphering the function of individual proteins, the set of data produced by proteomic methods represent the starting point for studying large-scale interactions that serve to discover general important properties for interaction participation. The fact that highly interactive proteins are often well conserved and/or essential or that homologous proteins, and, in particular, proteins with domains from the same family, tend to interact more frequently than others will likely improve the knowledge of their intrinsic properties. Thus, the understanding of the role these proteins play in the pathogenesis of respiratory diseases, while opening the door to much more powerful protein diagnostics, reinforces the linkage between basic medical research and clinical laboratory medicine. Addressing these concerns is obviously a top priority for the field, the ultimate goal of researchers being to understand the biology of disease and to translate this knowledge into the clinic.

There is no doubt that this branch of respiratory proteomics will have substantial improvement in the future.
