Bottom-Up Mass Spectrometry–Based Proteomics as an Investigative Analytical Tool for Discovery and Quantification of Proteins in Biological Samples

Ravi Amunugama, Richard Jones, Michael Ford, David Allen
2013 Advances in Wound Care  
Objective: The objective of this overview is to introduce bottom-up mass spectrometry (MS)-based proteomics approaches and strategies, widely used in other biomedical research fields, to the wound-healing research community. Approaches: Two major proteomics workflows are discussed: gel-based and gel-free chromatographic separation to reduce the complexity of the sample at protein and peptide level, respectively, prior to nano-liquid chromatographytandem mass spectrometry analysis. Other
more » ... es to discover less abundant proteins present in the sample, are also briefly discussed along with label-free and label-incorporated methods for protein quantification. Overall, the experimental workflows are designed and continually improved to increase the number of proteins identifiable and quantifiable. Discussion: Recent advances and improvements in all areas of proteomics workflow from sample preparation, to acquisition of massive amounts of data, to bioinformatics analysis have made this technology an indispensable tool for in-depth large-scale characterization of complex proteomes. This technology has been successfully applied in studies focusing on biomarker discovery, differential protein expression, protein-protein interactions, and post-translational modifications in complex biological samples such as cerebrospinal fluid, serum and plasma, and urine from patients. The publications from these studies have reported greater number of identified proteins, novel biomarker candidates, and post-translational modifications previously unknown. Conclusions: The qualitative and quantitative protein analysis of the protein population of wound tissues or fluids at different stages is important in wound healing research. Given the complexities and analytical challenges of these samples, MS-based proteomic workflows further improved with recent advances offer a powerful and attractive technology for this purpose. 2. Currette O, Buckhard PR, Sanchez JC, and Hochstrasser DF: State-of-the-art two dimensional gel electrophoresis: a key tool of proteomics research. Nat Protoc 2006; 1: 812. 3. Zanger RC, Varnum SM, and Bollinger NM: Studying cellular processes and detecting disease with protein microarrays. Drug Metab Rev 2005; 37: 473. 4. Janzi M, Odling J, Pan-Hammarstrom Q, Sundberg M, Lundeberg J, Uhlen M, Hammarstrom L, and Nilsson P: Serum microarrays for large scale screening of protein levels. Mol Cell Proteomics 2005; 4: 1942.
doi:10.1089/wound.2012.0384 pmid:24761338 pmcid:PMC3842888 fatcat:y65atkbifjhc5j57vpuvzk4nhm