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Systemic Lupus Erythematosus
Published in Jason Liebowitz, Philip Seo, David Hellmann, Michael Zeide, Clinical Innovation in Rheumatology, 2023
Vaneet K. Sandhu, Neha V. Chiruvolu, Daniel J. Wallace
Despite the 2019 EULAR/ACR criteria heavily emphasizing ANA as the entry criterion for the diagnosis of SLE, a positive ANA can be found in up to 30% of the general population and in other autoimmune conditions such as scleroderma, rheumatoid arthritis, Sjögren’s syndrome, and mixed connective tissue disease. ANA has been heavily criticized for its poor specificity,10 and there is emerging investigation into autoantigen arrays. Proteome microarray-based technology has been utilized for years to identify biomarkers in many diseases. Autoantigen arrays are used to screen and identify interactions between antigens and antibodies on a large scale.11 One of the benefits of this technology is that antibodies can be detected at a level of less than 1 ng/ml. Small samples, close to 1–2 microliters, can be obtained from serum, body fluids, or cell culture supernatant. Antibodies that bind to corresponding antigens on the array are detected using a fluorophore conjugate of second antibodies against different isotypes of autoantibodies (IgG, IgM, IGA, IgE). One of the marvels of autoantibody arrays is their capacity to detect hundreds of thousands of autoantibodies quantitatively and even prior to clinical onset of disease, thereby serving as an early diagnostic tool. Furthermore, quantification of antibodies may be helpful in monitoring disease activity and response to treatment. Data obtained from these arrays have demonstrated greater sensitivity in comparison to enzyme-linked immunosorbent assay (ELISA).12
Computational Drug Discovery and Development Along With Their Applications in the Treatment of Women-Associated Cancers
Published in Shazia Rashid, Ankur Saxena, Sabia Rashid, Latest Advances in Diagnosis and Treatment of Women-Associated Cancers, 2022
Rahul Kumar, Rakesh Kumar, Harsh Goel, Somorjit Singh Ningombam, Pranay Tanwar
A promising therapeutics target acts as a cornerstone in the process of target-based screening, and it could be either nucleic acid or a protein of different classes [7]. Over the past decades, the development of omics and its application have fostered the discovery of various disease-associated biomarkers [8–9]. Recently, a large number of potential molecular targets for cancer have been reported that can be explore for therapeutic action. There are generally two strategies involve in the identification process: (1) target discovery and (2) target deconvolution. Earlier strategies are based on elucidating the mechanism of disease and its related protein that can be used as a molecular target for further therapeutic intervention. Applications of genomics as well as transcriptomics approaches through high-throughput sequencing are widely used to gain insight into the disease and define population based on their genetic architecture [10]. Additionally, proteomics also plays a critical role in propelling the target discovery phase by recognizing aberrant protein expression. Further, protein microarray and mass spectrometry help in resolving the complexity of proteomes. [11–12].
Biochemical Markers in Ophthalmology
Published in Ching-Yu Cheng, Tien Yin Wong, Ophthalmic Epidemiology, 2022
Abdus Samad Ansari, Pirro G. Hysi
The term proteomics relates to the analysis of the entire protein complement of a cell, tissue, or organism under a specified set of defined conditions [138]. Proteomics is the process by which different proteins are studied to determine how they interact with each other and the role they play within an organism [139]. Proteomics has facilitated the reporting of an ever-increasing number of proteins and encompasses the investigation of proteomes from the overall level of protein activity, composition, and structure.
TMT-Based proteomics analysis of LPS-induced acute lung injury
Published in Experimental Lung Research, 2021
Shengsong Chen, Yi Zhang, Qingyuan Zhan
The proteome is defined as the complete set of proteins produced by the genome and thus encompasses all proteins produced by all cells with an organism.3,4 The rapid development of molecular technology, especially the rise of high-throughput proteomics technology, has provided new opportunities to identify disease biomarkers.3,4 Proteomics research can provide more biological information and reveal and explain the mechanisms of biological activities, as well as the in-depth core roles of physiological and pathological phenomena.3,4 As a discovery tool, proteomics can explore specific proteins related to diseases by comparing differences in protein expression levels and protein localization in cells, body fluids or tissues under different conditions, providing clues for the study of disease pathogenesis and identification of targets for treatment and drug development.3,4
Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade
Published in Expert Review of Proteomics, 2021
Jennie R. Lill, William R. Mathews, Christopher M. Rose, Markus Schirle
Factors governing the sensitivity of a mass spectrometric analysis include ionization efficiency, ion transfer efficiency into the vacuum system, and how ions are utilized/analyzed in the instrument [13]. Various mass spectrometric techniques have been employed to analyze increasingly less abundant proteins from a complex proteome. The analysis of individual protein or sets of proteins are reviewed in section (6.2.) but here we review the techniques available for global proteomic profiling, and the mass spectrometric approaches being utilized to achieve low level analyses here can be generalized into two approaches; a label-free approach, and a chemically tagged labeling technique, where reagents such as TMTs are employed for multiplexing samples and collectively amplifying signals from pooled analytes.
An overview of proteomic methods for the study of ‘cytokine storms’
Published in Expert Review of Proteomics, 2021
Paul David, Frederik J. Hansen, Adil Bhat, Georg F. Weber
MS has become one of the core technologies in proteomics. It performs qualitative and quantitative analysis of global proteome samples and has a vital role in gaining insights into cellular functions. In a classical proteomic workflow, the proteins are isolated by enrichment or prefractionation step and then digested by special proteases to produce smaller peptides [6]. These peptides are further concentrated and desalted, separated by high- performance liquid chromatography, ionized, and analyzed by MS. A tandem MS uses the mass to charge (m/z) ratio of peptide, and this measurement can be used to calculate the exact molecular weight of the peptide. Using MS the molecular signature of sepsis for cytokine storm was revealed by carrying out quantitative proteomics and lipidomics [7]. Another group deciphered the pharmacological mechanism of Ma Xing Shi Gan (MXSG) decoction against COVID-19, stating its protective role against the virus and also preventing cytokine storm and further lung injury [8]. The combination of MS with tandem mass tag (TMT) labeling by Thermo Fischer Scientific has expanded the measurement of single cells. With this system, the analysis throughput gets increased by multiplexing reagents that allow the analysis of several single cells in a single MS analysis.