Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity

Abstract

Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed.

An efficient biomarker panel for diagnosis of breast cancer using surface-enhanced laser desorption ionization time-of-flight mass spectrometry

“…SELDI-TOF-MS proteomic profiling has been proposed as a promising high-throughput technology with potential applications in BC screening, detection and prognostication. In some studies, detected ion peaks were identified as different due to variations in population demographics, stage of disease, collection and storage conditions of samples, and analytical procedures (11,32,33). Aside from the most common proteins (BC1, BC2, BC3 and CA15-3), many of the studied peaks had poor sensitivities and specificities and alone were insufficient to diagnose BC.…”

Proteomics in Diagnosis: Past, Present and Future

“…This technique is also useful for the determination of protein-protein interactions [46]. Table 4 summarizes the emerging techniques with their possible applications and advantages [45]. Preanalytical techniques especially sample storage, transportation and processing are the key factors for effective and unbiased results.…”

“…Multidimensional Protein Identification Technology (MudPIT) is yet another emerging proteomics technique. In the MudPIT approach, protein samples are subjected to sequence specific enzymatic digestion, usually with trypsin and endoproteinase lysC, and the resultant peptide mixtures are separated by strong cation exchange (SCX) and reversed phase (RP) high performance liquid chromatography (HPLC) which are then identified using mass spectrometry [45]. This technique is also useful for the determination of protein-protein interactions [46].…”

Extraction of intracellular protein from Glaciozyma antarctica for proteomics analysis

“…Recently, a number of proteomic studies on psychrophiles have been done to better understand the proteome level of the cellular process on how they can survive in cold environment [8,9]. Proteomics is a global assessment of cellular proteins expressed in a particular biological state [3,10]. This technology allows qualitative and quantitative measurements of many proteins that directly influence cellular biochemistry, thus provide accurate analysis of cellular states or system that changed during growth, development and response to environmental factors [11].…”