Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome

Protein abundance determination across multiple samples proved to be a daunting task and far fewer methods have been successfully devised for this purpose. Despite the technical challenges faced, protein abundance determination over multiple samples is still an area of interest. Herein, we introduce a new method for estimation of protein abundances in multiplexed samples (PAMUS). Protein abundance in the multiplexed sample comprising of the eight complex secretomes by Trichoderma reesei QM6a and Rut C30 grown in four different carbon sources, namely glucose, cellulose, starch, and a mixture of starch and cellulose was determined. For protein abundance in the multiplexed sample, exponentially modified protein abundance index (emPAI) was used. Using the PAMUS method, we estimated the abundance of extracellular lignocellulolytic proteins secreted by two T. reesei strains in response to various carbon sources. The results reveal that cellulose induces biosynthesis of cellulases. PAMUS analysis of the secretomes implicates T. reesei Rut C30 as a hyper cellulolytic strain and further revealed the optimum concentrations of each secreted enzyme during cellulosic substrate utilization. Our study demonstrates the plausible use of the PAMUS method for designing enzyme cocktails for optimum cellulose hydrolysis, and its potential applications in future studies involving other multiplexed biological samples. Biological significance Relative protein quantitation across multiple complex biological samples dominates the field of quantitative proteomics. Protein abundance determination across multiple samples, on the other hand, proves to be a daunting task and far fewer methods have been successfully devised for this purpose. Despite the technical challenges faced, protein abundance determination over multiple samples is still an area of interest as it provides unique information about the biological processes, and physiological states of particular disease, or that of microbes. This study introduces a new method of estimation of protein abundance in multiplexed samples (PAMUS) which is applied to study eight complex secretomes by Trichoderma reesei QM6a and Rut C30 grown in different carbon sources. The expression levels of proteins in the multiplexed eight complex secretome samples were determined by isobaric tags for relative and absolute quantitation (iTRAQ) reagents coupled with exponentially modified protein abundance index (emPAI) to calculate the abundance of each identified protein in eight conditions. This method with microbial secretome as an example facilitated a direct comparison of the abundance of proteins. This PAMUS could be applied for any multiple biological samples, for example, to study human disease to evaluate dynamic expression of proteins during disease progressions. (C) 2013 Elsevier B.V. All rights reserved.