The first editorial article by D. Josic entitled ‘Strategies for Complete Proteomic Analysis of Hydrophobic Proteins in Complex Biological Samples – Hyde-and Seek’ [3] discusses shortfalls in commonly performed analyses of proteins in complex mixtures, namely the incomplete extraction of hydrophobic proteins prior to mass spec analysis. Since highly abundant hydroplilic proteins often mask the less abundant hydrophobic moieties, new strategies for proteomic analysis had to be developed and are discussed in this paper. Recent developments in mass spectrometry, sample preparation and separation are the focus of the contribution by B. Willard and colleagues ‘Current Bioinformatics Challenges in Proteome Dynamics using Heavy Water-based Metabolic Labeling’ [4]. This elegantly and concisely written paper describes the present challenges of metabolome analysis using heavy-water based labeling and freely available software for advanced proteome dynamics studies recently developed by the authors at the University of Texas. Very much in line with the two previous papers, the editorial by S.S. Natarajan entitled ‘Analysis of Soybean Seed Proteins Using Proteomics’ discusses approaches and challenges in the field of agricultural proteome analysis stressing the importance of the proper protein extraction method from soybean seeds for subsequent analysis by 2 dimensional-polyacrylamide gel electrophoresis (PAGE) [5]. While these three editorials present fine descriptions of protein extraction methods, analytic strategies and challenges, future contributions to the JDMGP might place a stronger emphasis on the role of pre-analytical parameters [6].

Mao JH, Weier HUG (2014) Bioinformatics Applications in Biological and Clinical Studies. J Data Mining Genomics Proteomics 5:e114.

Link: https://www.omicsonline.org/open-access/bioinformatics-applications-in-biological-and-clinical-studies-2153-0602.1000e114.php?aid=27948

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