Editorial - Journal of Systems Biology & Proteome Research (2022) Volume 3, Issue 6
MEMBRANE PROTEOME FOR ANALYSIS BY LATER MASS SPECTROMETRY
Mohammad Fatemeh *
Department of Biological Sciences, University of Calgary, Canada
- *Corresponding Author:
- Mohammad Fatemeh
Department of Biological Sciences, University of Calgary, Canada
Received: 03-Nov-2022, Manuscript No. AASBPR-22-81767; Editor assigned: 04-Nov-2022, PreQC No. AASBPR-22-81767(PQ); Reviewed:16-Nov-2022, QC No. AASBPR-22-81767; Revised:18-Nov-2022, Manuscript No. AASBPR-22-81767(R); Published:25-Nov-2022, DOI:10.35841/aasbpr-3.6.126
Citation: Fatemeh M. Membrane proteome for analysis by later mass spectrometry. J Syst Bio Proteome Res. 2022;3(6):126
Proteins, glycolipids, and phospholipids make up cellular membranes, which are crucial for protecting and limiting metabolic processes within cells while also preserving cellular integrity and homeostasis. Membrane proteins serve as receptors, transporters, adhesion-anchors, enzymes, and many other crucial tasks. The determination of the plasma membrane (PM) proteome, resolution of membrane protein topology, establishment of numerous receptor protein complexes, identification of ligand-receptor pairs, and elucidation of signalling networks originating at the PM have all benefited from recent developments in proteomic mass spectrometry. Here, we discuss the remarkable acceleration of the development of a full membrane proteome by discovery-based proteomic algorithms. Most membrane proteins are less abundant and more hydrophobic than typical soluble proteins, which makes study of these proteins more challenging. The sample preparation, which includes the enrichment and dissolution of the membrane proteins, is crucial for the successful identification of membrane proteins. The enrichment of low-abundance membrane proteins at membrane and/or protein levels and the dissolution of hydrophobic membrane proteins have both been accomplished using a variety of established and recently developed techniques.
Transmembrane proteins are water insoluble, which makes them difficult to study using mass spectrometry and conventional biochemical methods, but not impossible (MS). In this review, we emphasise the importance of shotgun MS for hastening the discovery and investigation of membrane proteins. To better understand membrane protein structure, protein-protein interactions, and signalling networks that emerge from the membrane surface, we briefly discuss recent MS developments to determine the entire membrane proteome. Indeed, recent innovations in technology and methodology have lowered the obstacles that once prevented membrane. Undoubtedly, the under-representation of membrane proteins in large-scale proteomic datasets is due to the relatively low abundance of these proteins in un-fractionated samples. PM proteins are present in these databases, however they are harder to find than other proteins. A significant rise in the representation of PM proteins in large-scale data sets has been attributed to a number of recent technological developments, including enhanced sample preparation, equipment, and liquid chromatographic (LC) performance .
Even though the majority of membrane proteins cannot be accessed using conventional sample preparation methods, this is a subject that is very important to our discussion and has already been well reviewed. Shotgun MS is ideally suited for this challenge and may identify thousands of proteins in a single study. This is necessary in order to completely characterise membrane proteins. A significant advancement would be the identification of a comprehensive catalogue of membrane proteins, which might give a comprehensive overview of all the proteins at the PM .
The hydrophobicity, intricate post-translational modifications (PTMs), and low quantity of membrane proteins make it difficult to analyse them. The identification of membrane proteins is now more accurate than in earlier analyses due to improved instrument performance, making it possible to analyse complicated protein mixtures in greater detail. The identification of low abundance proteins in complicated mixtures can also be facilitated by optimising peptide chromatography and processing; this has aided in the thorough exploration of the PM proteome and represents an active area of research with considerable potential. With the commercial availability of column ovens, raising the temperature from degrees during micro LC has recently been demonstrated to increase the amount of membrane proteins detected in a typical analysis and should become standard practise. The identification of PM proteins has also been made easier by the use of MS-compatible detergents, which have been demonstrated to boost PM protein identifications and sequence coverage from the insoluble portion of rat brain homogenate .
Centrifugation makes it simple to enrich membrane proteins. Numerous biochemical enrichments followed by MS analysis have been used to answer the question of which proteins are connected to membranes in particular cell types. However, it is extremely difficult to isolate completely pure PM fractions due to the interconnectedness and complicated organisation of biological membranes. By lowering the complexity of the protein and thereby increasing the likelihood that less common PM proteins are found, fractionation and enrichment processes are straightforward and effective methods for analysing membrane proteins . A tissue of long-standing interest that is greatly enriched for membrane structures is the mammalian brain. Neurons within the central nervous system are linked together to form circuits in intricate configurations. Chemical synapses, which are specialised neuron-neuron junctions, are important membrane-enriched structures because they enable molecular communication between neurons. The Post-Synaptic Density (PSD), which has been repeatedly conducted with great, but perhaps insufficient, determination, is a shining illustration of the value of MS for study of biological membrane fractions .
MS has demonstrated to be an effective strategy for promoting discovery-based investigations, which will hasten our understanding of membrane proteins. The study of membrane proteins has been significantly impacted by these unexpected results, which have also given it a boost in novel and intriguing areas. In conclusion, MS identifies PM proteins in their whole, investigates PM architecture, maps PM protein-protein interactions, and clarifies PM signalling networks. In the immediate and long term, MS will continue to be the method of choice for studying membrane protein structure, signalling, and molecular interactions thanks to recent developments in shotgun proteomic apparatus and experimental design.
- Eichacker LA. Hiding behind hydrophobicity. Transmembrane segments in mass spectrometry. J Biol Chem. 2004;279(49):50915-50922.
- Weinglass AB, Whitelegge JP, Kaback HR. Integrating mass spectrometry into membrane protein drug discovery. Curr Opin Drug Discov Devel. 2004;7(5):589–599
- Bethani I, Skanland SS, Dikic I, et al. Spatial organization of transmembrane receptor signalling. EMBO J. 2010;29(16):2677-2688.
- Moebius J, et al. The human platelet membrane proteome reveals several new potential membrane proteins. Mol Cell Proteomics. 2005;4(11):1754-1761.
- 5. Nelson CJ, Hegeman AD, Harms AC, et al. A quantitative analysis of arabidopsis plasma membrane using trypsin-catalyzed (18)O labeling. Mol Cell Proteomics. 2006;5(8):1382-1395.