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Journal articles on the topic 'Proteomics'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Krieg, Rene C., Cloud P. Paweletz, Lance A. Liotta, and Emanuel F. Petricoin. "Clinical Proteomics for Cancer Biomarker Discovery and Therapeutic Targeting." Technology in Cancer Research & Treatment 1, no. 4 (2002): 263–72. http://dx.doi.org/10.1177/153303460200100407.

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As we emerge into the post-genome era, proteomics finds itself as the driving force field as we translate the nucleic acid information archive into understanding how the cell actually works and how disease processes operate. Even so, the traditionally held view of proteomics as simply cataloging and developing lists of the cellular protein repertoire of a cell are now changing, especially in the sub-discipline of clinical proteomics. The most relevant information archive to clinical applications and drug development involves the elucidation of the information flow of the cell; the “software” o

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Sukumaran, Pariveena, Ainun Aida Bahardin, Luqmanul Hakim Abdul Razak, and Mohd Harizal Senik. "Application of Proteomics in Alzheimer’s Disease: A Mini Review." SEPTEMBER 2023 19, no. 5 (2023): 317–30. http://dx.doi.org/10.47836/mjmhs.19.5.38.

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Alzheimer’s disease (AD) is classified as one of neurodegenerative disease caused by neuronal death. It is characterized as memory impairment, including the inability to produce new memories. Since AD has low treatment effectiveness, proteomics research opens possibilities for advancement. Proteomics is the study of proteomes produced by the disease-bearing host to identify and understand diseases. In this case, to investigate the use of protein as a reliable molecular entity and their involvement in AD. Therefore, this review focused on three main applications of proteomics; the potential use

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Mahajan, R., and P. Gupta. "Proteomics: taking over where genomics leaves off." Czech Journal of Genetics and Plant Breeding 46, No. 2 (2010): 47–53. http://dx.doi.org/10.17221/34/2009-cjgpb.

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The proteomic studies are simultaneously developed in several directions and significantly influence our notions on the capabilities of biological sciences. The need for proteomics research is necessary as there are certain genes in a cell that encode proteins with specific functions. Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life cycle and in different environmental conditions as every individual has one genome and many proteomes. Besides

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Sadeesh, Nithin, Mauro Scaravilli, and Leena Latonen. "Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes." Cancers 13, no. 19 (2021): 4829. http://dx.doi.org/10.3390/cancers13194829.

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Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate

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Sokolowska, Izabela, Armand G. Ngounou Wetie, Alisa G. Woods, and Costel C. Darie. "Applications of Mass Spectrometry in Proteomics." Australian Journal of Chemistry 66, no. 7 (2013): 721. http://dx.doi.org/10.1071/ch13137.

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Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, adva

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Walther, Tobias C., and Matthias Mann. "Mass spectrometry–based proteomics in cell biology." Journal of Cell Biology 190, no. 4 (2010): 491–500. http://dx.doi.org/10.1083/jcb.201004052.

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The global analysis of protein composition, modifications, and dynamics are important goals in cell biology. Mass spectrometry (MS)–based proteomics has matured into an attractive technology for this purpose. Particularly, high resolution MS methods have been extremely successful for quantitative analysis of cellular and organellar proteomes. Rapid advances in all areas of the proteomic workflow, including sample preparation, MS, and computational analysis, should make the technology more easily available to a broad community and turn it into a staple methodology for cell biologists.

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Oikonomou, Panos, Roberto Salatino, and Saeed Tavazoie. "In vivo mRNA display enables large-scale proteomics by next generation sequencing." Proceedings of the National Academy of Sciences 117, no. 43 (2020): 26710–18. http://dx.doi.org/10.1073/pnas.2002650117.

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Large-scale proteomic methods are essential for the functional characterization of proteins in their native cellular context. However, proteomics has lagged far behind genomic approaches in scalability, standardization, and cost. Here, we introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem. In vivo-expressed proteins are coupled with their encoding messenger RNAs (mRNAs) via a high-affinity stem-loop RNA binding domain interaction, enabling high-throughput identification of proteins with high sensitivity and specificity

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Soleymani, Nooshinmehr, Soheil Sadr, Cinzia Santucciu, et al. "Unveiling Novel Insights in Helminth Proteomics: Advancements, Applications, and Implications for Parasitology and Beyond." Biologics 4, no. 3 (2024): 314–44. http://dx.doi.org/10.3390/biologics4030020.

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Helminths have developed intricate mechanisms to survive and evade the host’s immune responses. Hence, understanding the excretory-secretory products (ESPs) by helminths is crucial for developing control tools, including drug targets, vaccines, and potential therapies for inflammatory and metabolic disorders caused by them. Proteomics, the large-scale analysis of proteins, offers a powerful approach to unravel the complex proteomes of helminths and gain insights into their biology. Proteomics, as a science that delves into the functions of proteins, has the potential to revolutionize clinical

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Stubbs, Keith A., and David J. Vocadlo. "Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes." Australian Journal of Chemistry 62, no. 6 (2009): 521. http://dx.doi.org/10.1071/ch09140.

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As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play role

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Duong, Van-An, and Hookeun Lee. "Bottom-Up Proteomics: Advancements in Sample Preparation." International Journal of Molecular Sciences 24, no. 6 (2023): 5350. http://dx.doi.org/10.3390/ijms24065350.

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Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, i

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Masood, Afshan, Hicham Benabdelkamel, and Assim Alfadda. "Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity." High-Throughput 7, no. 3 (2018): 27. http://dx.doi.org/10.3390/ht7030027.

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Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation te

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Thanasupawat, Thatchawan, Aleksandra Glogowska, Christopher Pascoe, et al. "Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes." International Journal of Molecular Sciences 22, no. 17 (2021): 9566. http://dx.doi.org/10.3390/ijms22179566.

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Malignant gliomas derive from brain glial cells and represent >75% of primary brain tumors. This includes anaplastic astrocytoma (grade III; AS), the most common and fatal glioblastoma multiforme (grade IV; GBM), and oligodendroglioma (ODG). We have generated patient-derived AS, GBM, and ODG cell models to study disease mechanisms and test patient-centered therapeutic strategies. We have used an aptamer-based high-throughput SOMAscan® 1.3K assay to determine the proteomic profiles of 1307 different analytes. SOMAscan® proteomes of AS and GBM self-organized into closely adjacent proteomes wh

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Schulze, W. "Environmental proteomics – what proteins from soil and surface water can tell us: a perspective." Biogeosciences Discussions 1, no. 1 (2004): 195–218. http://dx.doi.org/10.5194/bgd-1-195-2004.

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Abstract. Mass spectrometry based proteomics is widely used to study cellular processes in model organisms. However, it has not much been applied in environmental research because it was thought that free proteins would not be sufficiently stable in the environments. Based on recent observations that protein can readily be detected as a component of dissolve organic carbon, this article gives an overview about the possible use of proteomic methods in ecology and environmental sciences. At this stage, there are two areas of interest: (1) the identification of phylogenetic groups contributing to

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Ji, Qing, Fangshi Zhu, Xuan Liu, Qi Li, and Shi-bing Su. "Recent Advance in Applications of Proteomics Technologies on Traditional Chinese Medicine Research." Evidence-Based Complementary and Alternative Medicine 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/983139.

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Proteomics technology, a major component of system biology, has gained comprehensive attention in the area of medical diagnosis, drug development, and mechanism research. On the holistic and systemic theory, proteomics has a convergence with traditional Chinese medicine (TCM). In this review, we discussed the applications of proteomic technologies in diseases-TCM syndrome combination researches. We also introduced the proteomic studies on thein vivoandin vitroeffects and underlying mechanisms of TCM treatments using Chinese herbal medicine (CHM), Chinese herbal formula (CHF), and acupuncture.

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Komatsu, Setsuko, Myeong W. Oh, Hee Y. Jang, et al. "Proteomic Analyses of Soybean Root Tips During Germination." Protein & Peptide Letters 21, no. 12 (2014): 1308–19. http://dx.doi.org/10.2174/0929866521666140526152426.

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Plant root systems form complex networks with the surrounding soil environment and are controlled by both internal and external factors. To better understand the function of root tips of soybean during germination, three proteomic techniques were used to analyze the protein profiles of root tip cells. Proteins were extracted from the root tips of 4-dayold soybean seedlings and analyzed using two-dimensional (2D) gel electrophoresis-based proteomics, SDS-gel based proteomics, and gel-free proteomics techniques. A total of 121, 862, and 341 proteins were identified in root tips using the 2D gel-

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Gajahin Gamage, Nadeeka Thushari, Rina Miyashita, Kazutaka Takahashi, Shuichi Asakawa, and Jayan Duminda Mahesh Senevirathna. "Proteomic Applications in Aquatic Environment Studies." Proteomes 10, no. 3 (2022): 32. http://dx.doi.org/10.3390/proteomes10030032.

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Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biolog

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Rodríguez-Ulloa, Arielis, Jeovanis Gil, Yassel Ramos, et al. "Proteomic Study to Survey the CIGB-552 Antitumor Effect." BioMed Research International 2015 (2015): 1–18. http://dx.doi.org/10.1155/2015/124082.

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CIGB-552 is a cell-penetrating peptide that exertsin vitroandin vivoantitumor effect on cancer cells. In the present work, the mechanism involved in such anticancer activity was studied using chemical proteomics and expression-based proteomics in culture cancer cell lines. CIGB-552 interacts with at least 55 proteins, as determined by chemical proteomics. A temporal differential proteomics based on iTRAQ quantification method was performed to identify CIGB-552 modulated proteins. The proteomic profile includes 72 differentially expressed proteins in response to CIGB-552 treatment. Proteins rel

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Katamesh, Basant E., Pragyat Futela, Ann Vincent, et al. "Navigating the Proteomic Landscape of Menopause: A Review." Medicina 60, no. 9 (2024): 1473. http://dx.doi.org/10.3390/medicina60091473.

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Background and Objectives: Proteomics encompasses the exploration of protein composition, regulation, function, and pathways. Its influence spans diverse clinical fields and holds promise in addressing various women’s health conditions, including cancers, osteoporosis, and cardiovascular disorders. However, no comprehensive summary of proteomics and menopausal health exists. Our objective was to summarize proteomic profiles associated with diseases and disorders in peri- and postmenopausal women. Materials and Methods: We conducted a comprehensive search of databases including PubMed, Google S

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Yates, III, John R. "Recent technical advances in proteomics." F1000Research 8 (March 29, 2019): 351. http://dx.doi.org/10.12688/f1000research.16987.1.

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Mass spectrometry is one of the key technologies of proteomics, and over the last decade important technical advances in mass spectrometry have driven an increased capability for proteomic discovery. In addition, new methods to capture important biological information have been developed to take advantage of improving proteomic tools.

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Jain, K. K. "Oncoproteomics: State-of-the-Art." Technology in Cancer Research & Treatment 1, no. 4 (2002): 219–20. http://dx.doi.org/10.1177/153303460200100401.

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Proteomics is a promising approach in the identification of proteins and biochemical pathways involved in carcinogenesis. Proteomic technologies are now being incorporated in oncology in the post-genomic era. Cancer involves alterations in protein expression and provides a good model not only for detection of biomarkers but also their use in drug discovery. Proteomics has an impact on diagnostics as well as drug discovery. Genomics still remains an important approach but the value of proteomics lies in the fact that most of the diagnostics and drugs target proteins. The importance of applicati

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Thelen, Jay J., and Ján A. Miernyk. "The proteomic future: where mass spectrometry should be taking us." Biochemical Journal 444, no. 2 (2012): 169–81. http://dx.doi.org/10.1042/bj20110363.

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A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the ‘wet-bench’ aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis and gel-free or off-gel protein focusing, it has been the seminal advances in MS that have led to the ascension of this field. Recent improvements in sensitivity, mass accuracy and fragmentation have led to achievements previousl

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Tjalsma, Harold, Haike Antelmann, Jan D. H. Jongbloed, et al. "Proteomics of Protein Secretion by Bacillus subtilis: Separating the “Secrets” of the Secretome." Microbiology and Molecular Biology Reviews 68, no. 2 (2004): 207–33. http://dx.doi.org/10.1128/mmbr.68.2.207-233.2004.

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SUMMARY Secretory proteins perform a variety of important“ remote-control” functions for bacterial survival in the environment. The availability of complete genome sequences has allowed us to make predictions about the composition of bacterial machinery for protein secretion as well as the extracellular complement of bacterial proteomes. Recently, the power of proteomics was successfully employed to evaluate genome-based models of these so-called secretomes. Progress in this field is well illustrated by the proteomic analysis of protein secretion by the gram-positive bacterium Bacillus subtili

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Orsburn, Benjamin C. "Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric." Proteomes 9, no. 3 (2021): 34. http://dx.doi.org/10.3390/proteomes9030034.

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Proteomic technology has improved at a staggering pace in recent years, with even practitioners challenged to keep up with new methods and hardware. The most common metric used for method performance is the number of peptides and proteins identified. While this metric may be helpful for proteomics researchers shopping for new hardware, this is often not the most biologically relevant metric. Biologists often utilize proteomics in the search for protein regulators that are of a lower relative copy number in the cell. In this review, I re-evaluate untargeted proteomics data using a simple graphi

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Chang, Chiz-Tzung, Chao-Yuh Yang, Fuu-Jen Tsai, Shih-Yi Lin, and Chao-Jung Chen. "Mass Spectrometry-Based Proteomic Study Makes High-Density Lipoprotein a Biomarker for Atherosclerotic Vascular Disease." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/164846.

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High-density lipoprotein (HDL) is a lipid and protein complex that consists of apolipoproteins and lower level HDL-associated enzymes. HDL dysfunction is a factor in atherosclerosis and decreases patient survival. Mass spectrometry- (MS-) based proteomics provides a high throughput approach for analyzing the composition and modifications of complex HDL proteins in diseases. HDL can be separated according to size, surface charge, electronegativity, or apoprotein composition. MS-based proteomics on subfractionated HDL then allows investigation of lipoprotein roles in diseases. Herein, we review

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Fu, Jianbo, Yongchao Luo, Minjie Mou, et al. "Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection." Current Drug Targets 21, no. 1 (2019): 34–54. http://dx.doi.org/10.2174/1389450120666190821160207.

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Background: Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. Objective: The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker

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Kalvodova, Lucie. "Understanding the proteomes using non-proteomics approaches: Expanding the scope of PROTEOMICS." PROTEOMICS 17, no. 1-2 (2017): 1770013. http://dx.doi.org/10.1002/pmic.201770013.

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Hulahan, Taylor S., Laura Spruill, Elizabeth N. Wallace, et al. "Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics." International Journal of Molecular Sciences 25, no. 12 (2024): 6748. http://dx.doi.org/10.3390/ijms25126748.

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Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detai

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Pathade, Parag A., Vinod A. Bairagi, Yogesh S. Ahire, and Neela M. Bhatia. "Proteomics: Opportunities and Challenges." International Journal of Pharmaceutical Sciences and Nanotechnology 3, no. 4 (2011): 1165–72. http://dx.doi.org/10.37285/ijpsn.2010.3.4.1.

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‘‘Proteomics’’, is the emerging technology leading to high-throughput identification and understanding of proteins. Proteomics is the protein equivalent of genomics and has captured the imagination of biomolecular scientists, worldwide. Because proteome reveals more accurately the dynamic state of a cell, tissue, or organism, much is expected from proteomics to indicate better disease markers for diagnosis and therapy monitoring. Proteomics is expected to play a major role in biomedical research, and it will have a significant impact on the development of diagnostics and therapeutics for

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Huang, Huibin, and Jun He. "Proteomics in Natural Products: An Overview of Bioactive Compounds Research." Journal of Pharmaceutical and Biomedical Sciences 12, no. 02 (2022): 26–39. https://doi.org/10.5281/zenodo.7116089.

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Proteomics originated from 2-dimensional electrophoresis more than thirty years ago. Technological advances have made proteomics one of the most flourishing areas of modern biotechnology research. Proteomics mainly characterizes protein functions, protein–protein interactions, and protein modification in cells, tissues or animals. The integration of proteomic data helps to screen bioactive compounds, biomarkers of diseases, or signaling pathways in cells or the whole body. Natural products are valuable resources that contain a variety of bioactive compounds. However, the mechanisms of ac

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Mayr, Manuel, Ursula Mayr, Yuen-Li Chung, Xiaoke Yin, John R. Griffiths, and Qingbo Xu. "Vascular proteomics: Linking proteomic and metabolomic changes." PROTEOMICS 4, no. 12 (2004): 3751–61. http://dx.doi.org/10.1002/pmic.200400947.

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Adán-Jiménez, Javier, Alejandro Sánchez-Salvador, Esperanza Morato, Jose Carlos Solana, Begoña Aguado, and Jose M. Requena. "A Proteogenomic Approach to Unravel New Proteins Encoded in the Leishmania donovani (HU3) Genome." Genes 15, no. 6 (2024): 775. http://dx.doi.org/10.3390/genes15060775.

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The high-throughput proteomics data generated by increasingly more sensible mass spectrometers greatly contribute to our better understanding of molecular and cellular mechanisms operating in live beings. Nevertheless, proteomics analyses are based on accurate genomic and protein annotations, and some information may be lost if these resources are incomplete. Here, we show that most proteomics data may be recovered by interconnecting genomics and proteomics approaches (i.e., following a proteogenomic strategy), resulting, in turn, in an improvement of gene/protein models. In this study, we gen

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Poetsch, Ansgar, and María Inés Marchesini. "Proteomics of Brucella." Proteomes 8, no. 2 (2020): 8. http://dx.doi.org/10.3390/proteomes8020008.

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Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the molecular mechanisms underlying Brucella pathogenesis. Technological and methodological advancements such as increased instrument performance and multiplexed quantification have broadened the range of proteome studies, enabling new and improved analyses, providing deeper and more accurate prot

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Canetti, Diana, Francesca Brambilla, Nigel B. Rendell, et al. "Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres." Molecules 26, no. 7 (2021): 1913. http://dx.doi.org/10.3390/molecules26071913.

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Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for clinical diagnosis and for identifying the amyloid type. Currently, the proteomic approach is routinely used at National Amyloidosis Centre (NAC, London, UK) and Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR, Milan, Italy). Both centres are members of the European Prote

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Aziz, Ahmad Fudail Eiyad, Norhamizah Roshidi, Nurulhasanah Othman, Khayriyyah Mohd Hanafiah, and Norsyahida Arifin. "Application of Proteomics to the Study of the Therapeutics and Pathogenicity of Giardia duodenalis." Diagnostics 12, no. 11 (2022): 2744. http://dx.doi.org/10.3390/diagnostics12112744.

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Giardia duodenalis remains a neglected tropical disease. A key feature of the sustained transmission of Giardia is the ability to form environmentally resistant cysts. For the last 38 years, proteomics has been utilised to study various aspects of the parasite across different life cycle stages. Thirty-one articles have been published in PubMed from 2012 to 2022 related to the proteomics of G. duodenalis. Currently, mass spectrometry with LC-MS/MS and MALDI-TOF/TOF has been commonly utilised in proteomic analyses of Giardia, which enables researchers to determine potential candidates for diagn

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Alowoeshin, Samuel, Togaju Kuboye, Ifeanyi Ugwuanyi, et al. "Proteomics in the diagnosis and therapeutic management of human diseases: A review." European Journal of Scientific Research and Reviews 3, no. 1 (2025): 19. https://doi.org/10.5455/ejsrr.20250427010744.

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Abstract Proteomics is one of the major advances in understanding of human disease mechanisms, as well as, clinical applications with large scale study of proteins and functions. They include the traditional gel based technologies; the more advanced mass spectrometry and array based platforms, but the proteomic methods in this review are evolving from gel to mass spectrometry and then to array. Overall it is required to focus on the main branches such as structural, functional, clinical and metaproteomics related biomarker identification, disease diagnostic and therapeutic innovation. Proteomi

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Fedorov, Ivan I., Sergey A. Protasov, Irina A. Tarasova, and Mikhail V. Gorshkov. "Ultrafast Proteomics." Biochemistry (Moscow) 89, no. 8 (2024): 1349–61. http://dx.doi.org/10.1134/s0006297924080017.

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Abstract Current stage of proteomic research in the field of biology, medicine, development of new drugs, population screening, or personalized approaches to therapy dictates the need to analyze large sets of samples within the reasonable experimental time. Until recently, mass spectrometry measurements in proteomics were characterized as unique in identifying and quantifying cellular protein composition, but low throughput, requiring many hours to analyze a single sample. This was in conflict with the dynamics of changes in biological systems at the whole cellular proteome level upon the infl

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Eurich, Chris, Peter A. Fields, and Elizabeth Rice. "Proteomics: Protein Identification Using Online Databases." American Biology Teacher 74, no. 4 (2012): 250–55. http://dx.doi.org/10.1525/abt.2012.74.4.8.

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Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory course. Students upload files of “unknown” proteins from our public website, enter them into a proteomics search engine (Mascot), identify the proteins, and use additional proteomics websites to learn about their functions and three-dimensional struct

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Ouni, Emna, Didier Vertommen, and Christiani A. Amorim. "The Human Ovary and Future of Fertility Assessment in the Post-Genome Era." International Journal of Molecular Sciences 20, no. 17 (2019): 4209. http://dx.doi.org/10.3390/ijms20174209.

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Proteomics has opened up new avenues in the field of gynecology in the post-genome era, making it possible to meet patient needs more effectively and improve their care. This mini-review aims to reveal the scope of proteomic applications through an overview of the technique and its applications in assisted procreation. Some of the latest technologies in this field are described in order to better understand the perspectives of its clinical applications. Proteomics seems destined for a promising future in gynecology, more particularly in relation to the ovary. Nevertheless, we know that reprodu

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Kalantari, Shiva, Ameneh Jafari, Raheleh Moradpoor, Elmira Ghasemi, and Ensieh Khalkhal. "Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases." International Journal of Proteomics 2015 (November 29, 2015): 1–17. http://dx.doi.org/10.1155/2015/782798.

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Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunogl

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Vidal, Bernardo C., Joseph V. Bonventre, and Stephen I-Hong Hsu. "Towards the application of proteomics in renal disease diagnosis." Clinical Science 109, no. 5 (2005): 421–30. http://dx.doi.org/10.1042/cs20050085.

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Proteomics is widely envisioned as playing a significant role in the translation of genomics to clinically useful applications, especially in the areas of diagnostics and prognostics. In the diagnosis and treatment of kidney disease, a major priority is the identification of disease-associated biomarkers. Proteomics, with its high-throughput and unbiased approach to the analysis of variations in protein expression patterns (actual phenotypic expression of genetic variation), promises to be the most suitable platform for biomarker discovery. Combining such classic analytical techniques as two-d

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Dunkley, T. P. J., P. Dupree, R. B. Watson, and K. S. Lilley. "The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana." Biochemical Society Transactions 32, no. 3 (2004): 520–23. http://dx.doi.org/10.1042/bst0320520.

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Organelle proteomics is the analysis of the protein contents of a subcellular compartment. Proteins identified in subcellular proteomic studies can only be assigned to an organelle if there are no contaminants present in the sample preparation. As a result, the majority of plant organelle proteomic studies have focused on the chloroplast and mitochondria, which can be isolated relatively easily. However, the isolation of components of the endomembrane system is far more difficult due to their similar sizes and densities. For this reason, quantitative proteomics methods are being developed to e

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Wu, Haifeng M., Ming Jin, and Clay B. Marsh. "Toward functional proteomics of alveolar macrophages." American Journal of Physiology-Lung Cellular and Molecular Physiology 288, no. 4 (2005): L585—L595. http://dx.doi.org/10.1152/ajplung.00305.2004.

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Alveolar macrophages (AM) belong to a phenotype of macrophages with distinct biological functions and important pathophysiological roles in lung health and disease. The molecular details determining AM differentiation from blood monocytes and AM roles in lung homeostasis are largely unknown. With the use of different technological platforms, advances in the field of proteomics have made it possible to search for differences in protein expression between AM and their precursor monocytes. Proteome features of each cell type provide new clues into understanding mononuclear phagocyte biology. In-d

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Sharma, Vipin Kumar, and Ravi Kumar. "Current applications of proteomics: a key and novel approach." International Journal of Advances in Medicine 6, no. 6 (2019): 1953. http://dx.doi.org/10.18203/2349-3933.ijam20195259.

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Proteomics represented vital applications of technologies in the identification and quantification of high to moderate proteins (cellular signalling networks) found in biological matrix such as tissues, cells and fluids. Proteomics based technical knowledge is applied and verified in several preclinical research settings such as invention of diagnostic markers for specific disease and have shown to be increased in clinical applications. Extensive studies on proteomics resulted in detection of biomarkers that have been highly advanced in using diseases for cancer, lungs, cardiovascular, renal a

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Yihunie, Fanuel Bizuayehu, Mequanint Addisu Belete, Gizachew Fentahun, Solomon Getachew, and Teshager Dubie. "Diagnostic and Therapeutic Application of Proteomics in Infectious Disease." Advances in Cell and Gene Therapy 2023 (August 24, 2023): 1–6. http://dx.doi.org/10.1155/2023/5510791.

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The study of an organism’s genome, often known as “genomics,” has advanced quickly, producing a wealth of publicly accessible genetic data. Despite how valuable the genome is; proteins essentially control most aspects of cell function. Proteomics, or the comprehensive study of proteins, has emerged as an important technology for disease characterization, diagnosis, prognosis, drug development, and therapy. Proteomics technologies are now used to support the diagnosis and treatment of both infectious and noninfectious diseases. Nevertheless, it is more difficult to describe a proteomic profile

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Senavirathna, Lakmini, Cheng Ma, Ru Chen, and Sheng Pan. "Spectral Library-Based Single-Cell Proteomics Resolves Cellular Heterogeneity." Cells 11, no. 15 (2022): 2450. http://dx.doi.org/10.3390/cells11152450.

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Dissecting the proteome of cell types and states at single-cell resolution, while being highly challenging, has significant implications in basic science and biomedicine. Mass spectrometry (MS)-based single-cell proteomics represents an emerging technology for system-wide, unbiased profiling of proteins in single cells. However, significant challenges remain in analyzing an extremely small amount of proteins collected from a single cell, as a proteome-wide amplification of proteins is not currently feasible. Here, we report an integrated spectral library-based single-cell proteomics (SLB-SCP)

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Cutillas, Pedro, Alma Burlingame, and Robert Unwin. "Proteomic Strategies and Their Application in Studies of Renal Function." Physiology 19, no. 3 (2004): 114–19. http://dx.doi.org/10.1152/nips.01515.2003.

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Proteomics is a promising new tool for functional genomics. In addition to two-dimensional gel electrophoresis, other methods that are based on liquid chromatography and mass spectrometry are now available to study proteins. In this brief article, we review the strengths and limitations of the proteomic approaches currently available to the researcher, and we provide examples of how proteomics has been, and can in the future be, used to study the kidney.

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Jiang, Will, Jennifer C. Jones, Uma Shankavaram, Mary Sproull, Kevin Camphausen, and Andra V. Krauze. "Analytical Considerations of Large-Scale Aptamer-Based Datasets for Translational Applications." Cancers 14, no. 9 (2022): 2227. http://dx.doi.org/10.3390/cancers14092227.

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The development and advancement of aptamer technology has opened a new realm of possibilities for unlocking the biocomplexity available within proteomics. With ultra-high-throughput and multiplexing, alongside remarkable specificity and sensitivity, aptamers could represent a powerful tool in disease-specific research, such as supporting the discovery and validation of clinically relevant biomarkers. One of the fundamental challenges underlying past and current proteomic technology has been the difficulty of translating proteomic datasets into standards of practice. Aptamers provide the capaci

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Geng, Ruihui, Zhaoshen Li, Shude Li, and Jun Gao. "Proteomics in Pancreatic Cancer Research." International Journal of Proteomics 2011 (August 14, 2011): 1–5. http://dx.doi.org/10.1155/2011/365350.

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Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathoge

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Nichols, Heather L., Ning Zhang, and Xuejun Wen. "Proteomics and genomics of microgravity." Physiological Genomics 26, no. 3 (2006): 163–71. http://dx.doi.org/10.1152/physiolgenomics.00323.2005.

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Many serious adverse physiological changes occur during spaceflight. In the search for underlying mechanisms and possible new countermeasures, many experimental tools and methods have been developed to study microgravity caused physiological changes, ranging from in vitro bioreactor studies to spaceflight investigations. Recently, genomic and proteomic approaches have gained a lot of attention; after major scientific breakthroughs in the fields of genomics and proteomics, they are now widely accepted and used to understand biological processes. Understanding gene and/or protein expression is t

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Vu, Hung M., Ju Yeon Lee, Yongmin Kim, et al. "Exploring the feasibility of a single-protoplast proteomic analysis." Journal of Analytical Science and Technology 15, no. 1 (2024). http://dx.doi.org/10.1186/s40543-024-00457-x.

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Abstract Background Recent advances in high-resolution mass spectrometry have now enabled the study of proteomes at the single-cell level, offering the potential to unveil novel aspects of cellular processes. Remarkably, there has been no prior attempt to investigate single-plant cell proteomes. In this study, we aimed to explore the feasibility of conducting a proteomic analysis on individual protoplasts. Findings As a result, our analysis identified 978 proteins from the 180 protoplasts, aligning with well-known biological processes in plant leaves, such as photosynthetic electron transport

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