Evolving Horizons in Proteomics Technology: Transitioning from Gel Electrophoresis to Next-Generation Methods
, Manuscript No. ejbi-24-123936; , Pre QC No. ejbi-24-123936; , Manuscript No. ejbi-24-123936; Published: 30-Dec-2023
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Introduction
Proteomics, the study of proteins and their functions within biological systems, has undergone a remarkable transformation propelled by technological advancements. Over the years, proteomics technology has evolved from traditional methods like gel electrophoresis to sophisticated, high-throughput techniques that enable comprehensive analyses of complex protein landscapes. This article traces the trajectory of proteomics technology, highlighting the revolutionary shifts that have redefined our understanding of proteins and their roles in biological processes [1].
Emergence of gel electrophoresis
Gel electrophoresis, a foundational technique in proteomics, revolutionized the field by allowing the separation of proteins based on their molecular weight. Introduced in the mid-20th century, this method involved the migration of proteins through a gel matrix under an electric field. Polyacrylamide gel electrophoresis (PAGE) and its variations, including sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), became standard tools for protein separation and analysis [2].
Two-Dimensional Gel Electrophoresis (2D-PAGE)
The advent of two-dimensional gel electrophoresis (2D-PAGE) marked a significant leap forward in proteomics technology. By combining isoelectric focusing (separating proteins by charge) with SDS-PAGE (separating proteins by size), 2D-PAGE enabled the separation of complex protein mixtures with greater resolution. Researchers could visualize hundreds to thousands of proteins simultaneously, laying the groundwork for identifying and characterizing proteins in diverse biological samples [3].
Mass spectrometry revolutionizes proteomics:
Mass spectrometry (MS), a transformative technology in proteomics, emerged as a powerful tool for protein identification and characterization. Coupled with advancements in liquid chromatography (LC), MS enables the precise measurement of mass-to-charge ratios of peptides or proteins. Tandem mass spectrometry (MS/MS) facilitates protein sequencing and identification by fragmenting peptides and analysing their mass spectra.
Shotgun proteomics, an approach that involves digesting proteins into peptides and analysing them using high-throughput mass spectrometry, brought a paradigm shift in proteomics research. Liquid chromatography-tandem mass spectrometry (LC-MS/ MS) in shotgun proteomics allows for the identification and quantification of a vast number of proteins from complex samples. This technique significantly enhanced the throughput and depth of proteome analysis, enabling comprehensive studies in various biological contexts [4, 5].
Label-free quantitative proteomics
Label-free quantitative proteomics emerged as an alternative to traditional labelling methods. It relies on comparing the abundance of peptides or proteins across samples based on their spectral counts or chromatographic peak intensities. Label-free approaches offer advantages in terms of simplicity, dynamic range, and reduced experimental variability, making them increasingly popular in quantitative proteomics studies [6].
Targeted proteomics and Selected Reaction Monitoring (SRM)
Targeted proteomics techniques, such as Selected Reaction Monitoring (SRM) or parallel reaction monitoring (PRM), focus on the precise quantification of specific proteins or peptides of interest. Unlike shotgun proteomics, targeted approaches allow for highly accurate and sensitive quantification of predefined protein targets. These methods are valuable for validating biomarkers, studying protein signaling pathways, and monitoring specific protein changes in diseases [7].
High-throughput proteomics platforms
Advancements in high-throughput proteomics platforms, including top-down and bottom-up proteomics, have expanded the scope and depth of proteome analysis. Top-down proteomics involves the analysis of intact proteins, providing insights into protein isoforms and post-translational modifications. Bottom-up proteomics, on the other hand, involves digesting proteins into peptides for analysis, offering comprehensive coverage of the proteome [8].
Integration of proteomics with multi-omics approaches
The integration of proteomics with other omics technologies, such as genomics, transcriptomics, metabolomics, and interactomics, facilitates a holistic understanding of biological systems. Multi-omics approaches enable researchers to unravel intricate molecular networks, interactions, and regulatory mechanisms, providing a more comprehensive view of cellular processes and disease mechanisms [9].
Future directions and challenge
Continued advancements in proteomics technology focus on enhancing sensitivity, throughput, and data analysis capabilities. Innovations in instrumentation, computational tools, and data integration strategies will drive the field towards deeper insights into protein function, dynamics, and interactions.
Challenges persist in proteomics, including data complexity, standardization of protocols, and the need for robust bioinformatics tools for data analysis and interpretation. Overcoming these challenges will further propel the field towards uncovering the complexities of the proteome and its relevance to health, disease, and biological functions [10].
Conclusion
From the foundational techniques of gel electrophoresis to the era of high-throughput mass spectrometry and label-free quantitation, proteomics technology has undergone a transformative journey. These advancements have empowered researchers to delve deeper into the intricacies of the proteome, unraveling the roles of proteins in health, disease, and cellular functions. As proteomics continues to evolve, its integration with multi-omics approaches holds the promise of unveiling the complexities of biological systems at an unprecedented scale, fostering new frontiers in scientific discovery and innovation.
References
- Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009; 19:1622–1629.
- Amaral AJ, Megens HJ, Kerstens HH, Heuven HC, Dibbits B, et al. Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics. 2009; 10:374.
- Amstutz U, Andrey-Zürcher G, Suciu D, Jaggi R, Häberle J, et al. Sequence capture and next-generation resequencing of multiple tagged nucleic acid samples for mutation screening of urea cycle disorders. Clin Chem. 2011; 57:102–111.
- Andersson L, Haley CS, Ellegren H, Knott SA, Johansson M, et al. Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science. 1994; 263(5154):1771-4.
- Ansorge W, Sproat BS, Stegemann J, Schwager C. A non-radioactive automated method for DNA sequence determination. J Biochem Biophys Methods.1986; 13:315–323.
- Ansorge W, Sproat B, Stegemann J, Schwager C, Zenke M. Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acids Res. 1987; 15(11):4593-602.
- Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, et al. The sheep genome reference sequence: a work in progress. Ani Gen. 2010; 41(5):449-53.
- Astier Y, Braha O, Bayley H. Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5 ‘-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J Am Chem Soc . 2006; 128(5):1705-10.
- Bansal V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics. 2010; 26(12):i318-24.
- Bashamboo A, Ledig S, Wieacker P, Achermann JC, McElreavey K. New technologies for the identification of novel genetic markers of disorders of sex development (DSD). Sex Dev. 2010; 4(4-5):213-24.
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