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Journal articles on the topic 'Proteome proteomics'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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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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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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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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Burat, Bastien, Audrey Reynaerts, Dominique Baiwir, et al. "Characterization of the Human Eccrine Sweat Proteome—A Focus on the Biological Variability of Individual Sweat Protein Profiles." International Journal of Molecular Sciences 22, no. 19 (2021): 10871. http://dx.doi.org/10.3390/ijms221910871.

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The potential of eccrine sweat as a bio-fluid of interest for diagnosis and personalized therapy has not yet been fully evaluated, due to the lack of in-depth sweat characterization studies. Thanks to recent developments in omics, together with the availability of accredited sweat collection methods, the analysis of human sweat may now be envisioned as a standardized, non-invasive test for individualized monitoring and personalized medicine. Here, we characterized individual sweat samples, collected from 28 healthy adult volunteers under the most standardized sampling methodology, by applying

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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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Solovyeva, Elizaveta M., Julia A. Bubis, Irina A. Tarasova, et al. "On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics." Biochemistry (Moscow) 87, no. 11 (2022): 1342–53. http://dx.doi.org/10.1134/s000629792211013x.

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Abstract Protein quantitation in tissue cells or physiological fluids based on liquid chromatography/mass spectrometry is one of the key sources of information on the mechanisms of cell functioning during chemotherapeutic treatment. Information on significant changes in protein expression upon treatment can be obtained by chemical proteomics and requires analysis of the cellular proteomes, as well as development of experimental and bioinformatic methods for identification of the drug targets. Low throughput of whole proteome analysis based on liquid chromatography and tandem mass spectrometry

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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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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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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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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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Gerszten, Robert E., Frank Accurso, Gordon R. Bernard, et al. "Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs." American Journal of Physiology-Lung Cellular and Molecular Physiology 295, no. 1 (2008): L16—L22. http://dx.doi.org/10.1152/ajplung.00044.2008.

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The emerging scientific field of proteomics encompasses the identification, characterization, and quantification of the protein content or proteome of whole cells, tissues, or body fluids. The potential for proteomic technologies to identify and quantify novel proteins in the plasma that can function as biomarkers of the presence or severity of clinical disease states holds great promise for clinical use. However, there are many challenges in translating plasma proteomics from bench to bedside, and relatively few plasma biomarkers have successfully transitioned from proteomic discovery to rout

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Lapinel, Nicole, Jessie Guidry, Mary Varkey, Manish Rijal, Arnold Zea, and Juzar Ali. "76215 Implementation of Proteomics as a Diagnostic tool for Nontuberculous mycobacteria (NTM) Infection." Journal of Clinical and Translational Science 5, s1 (2021): 140–41. http://dx.doi.org/10.1017/cts.2021.759.

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ABSTRACT IMPACT: Implementation of proteomics as a diagnostic tool for Nontuberculous mycobacteria (NTM) infection can provide a more accurate, efficient and cost-effective means for effectively diagnosing disease and enacting timely management decisions which can revolutionize patient care. OBJECTIVES/GOALS: Proteomic analysis is a proven diagnostic modality enabling rapid identification of microorganisms. We sought to apply proteomics to detect proteins unique to the most clinically relevant NTM. We then determined whether these unique proteomes could be used to successfully identify NTM spe

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Pruess, Manuela, and Rolf Apweiler. "Bioinformatics Resources for In Silico Proteome Analysis." Journal of Biomedicine and Biotechnology 2003, no. 4 (2003): 231–36. http://dx.doi.org/10.1155/s1110724303209219.

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In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species—mainly the human—have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, character

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Unwin, Richard D., Duncan L. Smith, David Blinco, et al. "Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells." Blood 107, no. 12 (2006): 4687–94. http://dx.doi.org/10.1182/blood-2005-12-4995.

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Abstract The proteome is determined by rates of transcription, translation, and protein turnover. Definition of stem cell populations therefore requires a stem cell proteome signature. However, the limit to the number of primary cells available has restricted extensive proteomic analysis. We present a mass spectrometric method using an isobaric covalent modification of peptides for relative quantification (iTRAQ), which was employed to compare the proteomes of approximately 1 million long-term reconstituting hematopoietic stem cells (Lin–Sca+Kit+; LSK+) and non–long-term reconstituting progeni

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Jenkins, Conor, and Benjamin Orsburn. "The Cannabis Proteome Draft Map Project." International Journal of Molecular Sciences 21, no. 3 (2020): 965. http://dx.doi.org/10.3390/ijms21030965.

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Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these

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Yaacob, Mohamad Fakhri, Nur Anisah Johari, Alya Nur Athirah Kamaruzzaman, and Mohd Fakharul Zaman Raja Yahya. "Mass Spectrometry-Based Proteomic Investigation of Heterogeneous Biofilms: A Review." Scientific Research Journal 18, no. 2 (2021): 67–87. http://dx.doi.org/10.24191/srj.v18i2.11718.

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Biofilm represents a major public health concern. It is a highly structured and heterogeneous microbial population that is well protected by a hydrated extracellular matrix. In most cases, the difficulties in combating a wide spectrum of biofilm-associated diseases are due to the presence of dormant cells and differential molecular expression. Proteomics is the large-scale and systematic study of cellular proteome expression at any given time by mass spectrometry. It allows high-sensitivity and high-specificity identification of differentially expressed proteins in the biofilms. Over the past

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Zhan, Xianquan, Biao Li, Xiaohan Zhan, Hartmut Schlüter, Peter R. Jungblut, and Jens R. Coorssen. "Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level." Proteomes 7, no. 4 (2019): 36. http://dx.doi.org/10.3390/proteomes7040036.

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Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical

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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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Kozlowski, Lukasz Pawel. "Proteome-pI 2.0: proteome isoelectric point database update." Nucleic Acids Research 50, no. D1 (2021): D1535—D1540. http://dx.doi.org/10.1093/nar/gkab944.

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Abstract Proteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. The isoelectric point—the pH at which a particular molecule carries no net electrical charge—is an important parameter for many analytical biochemistry and proteomics techniques. Additionally, it can be obtained directly from the pKa values of individual charged residues of the protein. The Proteome-pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release)

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Zecha, Jana, Chien-Yun Lee, Florian P. Bayer, et al. "Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing." Molecular & Cellular Proteomics 19, no. 9 (2020): 1503–22. http://dx.doi.org/10.1074/mcp.ra120.002164.

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As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their p

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Agarwal, Ashok, Manesh Kumar Panner Selvam, and Saradha Baskaran. "Proteomic Analyses of Human Sperm Cells: Understanding the Role of Proteins and Molecular Pathways Affecting Male Reproductive Health." International Journal of Molecular Sciences 21, no. 5 (2020): 1621. http://dx.doi.org/10.3390/ijms21051621.

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Human sperm proteomics research has gained increasing attention lately, which provides complete information about the functional state of the spermatozoa. Changes in the sperm proteome are evident in several male infertility associated conditions. Global proteomic tools, such as liquid chromatography tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight, are used to profile the sperm proteins to identify the molecular pathways that are defective in infertile men. This review discusses the use of proteomic techniques to analyze the spermatozoa proteome. It also

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Balotf, Sadegh, Richard Wilson, Robert S. Tegg, David S. Nichols, and Calum R. Wilson. "Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions." Proteomes 10, no. 1 (2022): 5. http://dx.doi.org/10.3390/proteomes10010005.

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The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant–pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state o

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Bespyatykh, Ju A., E. A. Shitikov, and E. N. Ilina. "Proteomics for the Investigation of Mycobacteria." Acta Naturae 9, no. 1 (2017): 15–25. http://dx.doi.org/10.32607/20758251-2017-9-1-15-25.

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The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is w

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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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Campanati, Anna, Emanuela Martina, Federico Diotallevi, et al. "Saliva Proteomics as Fluid Signature of Inflammatory and Immune-Mediated Skin Diseases." International Journal of Molecular Sciences 22, no. 13 (2021): 7018. http://dx.doi.org/10.3390/ijms22137018.

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Saliva is easy to access, non-invasive and a useful source of information useful for the diagnosis of serval inflammatory and immune-mediated diseases. Following the advent of genomic technologies and -omic research, studies based on saliva testing have rapidly increased and human salivary proteome has been partially characterized. As a proteomic protocol to analyze the whole saliva proteome is not currently available, the most common aim of the proteomic analysis is to discriminate between physiological and pathological conditions. The salivary proteome has been initially investigated in seve

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Gao, Xiaoguang, Dandan Zhao, Lin Wang, et al. "Proteomic Changes in Sarcoplasmic and Myofibrillar Proteins Associated with Color Stability of Ovine Muscle during Post-Mortem Storage." Foods 10, no. 12 (2021): 2989. http://dx.doi.org/10.3390/foods10122989.

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The objective of this study was to investigate the proteomic characteristics for the sarcoplasmic and myofibrillar proteomes of M. longissimus lumborum (LL) and M. psoasmajor (PM) from Small-tailed Han Sheep. During post-mortem storage periods (1, 3, and 5 days), proteome analysis was applied to elucidate sarcoplasmic and myofibrillar protein changes in skeletal muscles with different color stability. Proteomic results revealed that the identified differentially abundant proteins were glycolytic enzymes, energy metabolism enzymes, chaperone proteins, and structural proteins. Through Pearson’s

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Bonomini, Mario, Luisa Pieroni, Maurizio Ronci, Vittorio Sirolli, and Andrea Urbani. "Blood Cell Proteomics in Chronic Kidney Disease." Open Urology & Nephrology Journal 11, no. 1 (2018): 28–38. http://dx.doi.org/10.2174/1874303x01811010028.

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Background: The uremic syndrome mimes a systemic poisoning with the retention of numerous compounds which are normally removed by the kidney. The study of proteins and peptides, or proteomics, represents an important field of research for the investigation of blood and blood diseases. Methods and Materials: We focused our review on the results of proteomic investigations on blood cells of uremic patients with particular regard to the study of red blood cells, platelets, and monocytes. Results: In literature there are few, preliminary studies on platelets and monocytes while the knowledge on ur

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Bhawal, Ruchika, Ann L. Oberg, Sheng Zhang, and Manish Kohli. "Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer." Cancers 12, no. 9 (2020): 2428. http://dx.doi.org/10.3390/cancers12092428.

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Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding

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Mirza, Shama P., and Michael Olivier. "Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry." Physiological Genomics 33, no. 1 (2008): 3–11. http://dx.doi.org/10.1152/physiolgenomics.00292.2007.

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Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification

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Matialu, Dewi D. L., Erwin G. Kristanto, and Johannis F. Mallo. "Proteomics sebagai Metode Identifikasi dalam Ilmu Kedokteran Forensik." Jurnal Biomedik:JBM 14, no. 1 (2022): 61. http://dx.doi.org/10.35790/jbm.v14i1.37343.

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Abstract: DNA analysis is the gold standard in forensic identification, however there are some circumstances in which DNA has been degraded or uninformative that make proteomics has the potential to be an alternative method of forensic identification. This study used a literature review method using four databases (Pubmed, ScienceDirect, Proquest, and SpringerLink). The keywords used in the data search are Proteomics OR Analysis Proteome OR Protein-based Identification AND Forensic Identification. The data selection process using inclusion and exclusion criteria, resulted in 10 literatures (re

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Maxwell, Karen L., and Lori Frappier. "Viral Proteomics." Microbiology and Molecular Biology Reviews 71, no. 2 (2007): 398–411. http://dx.doi.org/10.1128/mmbr.00042-06.

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SUMMARY Viruses have long been studied not only for their pathology and associated disease but also as model systems for molecular processes and as tools for identifying important cellular regulatory proteins and pathways. Recent advances in mass spectrometry methods coupled with the development of proteomic approaches have greatly facilitated the detection of virion components, protein interactions in infected cells, and virally induced changes in the cellular proteome, resulting in a more comprehensive understanding of viral infection. In addition, a rapidly increasing number of high-resolut

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Daniel-Fischer, Lisa, Isabel J. Sobieszek, Anja Wagner, et al. "In-Depth Analysis of the Extracorporeal Proteome Adsorbed to Dialysis Membranes during Hemodialysis." Membranes 12, no. 11 (2022): 1120. http://dx.doi.org/10.3390/membranes12111120.

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Used hemodialysis membranes (HD-M) are a valuable reservoir of biological information. Proteins bind to HD-M, but whether this process depends on the type of membrane or patient factors or selectively affects specific protein classes has not been adequately elucidated. State-of-the-art proteomics techniques are capable of identifying and quantifying this therapy-specific subproteome to enable the analysis of disease- or membrane-induced pathophysiologies. We demonstrate the feasibility of the deep proteomic characterization of the extracorporeal proteome adsorbed to HD-M. A shotgun proteomics

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Moghieb, Ahmed, Geremy Clair, Hugh D. Mitchell, et al. "Time-resolved proteome profiling of normal lung development." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 1 (2018): L11—L24. http://dx.doi.org/10.1152/ajplung.00316.2017.

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Biochemical networks mediating normal lung morphogenesis and function have important implications for ameliorating morbidity and mortality in premature infants. Although several transcript-level studies have examined normal lung development, corresponding protein-level analyses are lacking. Here we performed proteomics analysis of murine lungs from embryonic to early adult ages to identify the molecular networks mediating normal lung development. We identified 8,932 proteins, providing a deep and comprehensive view of the lung proteome. Analysis of the proteomics data revealed discrete modules

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Maguire, P. B., M. Foy, and D. J. Fitzgerald. "Using proteomics to identify potential therapeutic targets in platelets." Biochemical Society Transactions 33, no. 2 (2005): 409–12. http://dx.doi.org/10.1042/bst0330409.

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Proteomics has provided powerful new insights into the complex events of the anucleate platelet and has revealed many potential protein targets in the search for suitable agents for thrombotic disease. In the present study, we summarize recent proteomic approaches to analyse specific platelet subproteomes, such as the platelet releasate, the platelet phosphotyrosine proteome and characterization of the proteins associated with membrane lipid rafts.

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Han, Mee-Jung, and Sang Yup Lee. "The Escherichia coli Proteome: Past, Present, and Future Prospects." Microbiology and Molecular Biology Reviews 70, no. 2 (2006): 362–439. http://dx.doi.org/10.1128/mmbr.00036-05.

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SUMMARY Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced pro

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Vítámvás, P., K. Kosová, and I. T. Prášil. "Proteome analysis in plant stress research: a review." Czech Journal of Genetics and Plant Breeding 43, No. 1 (2008): 1–6. http://dx.doi.org/10.17221/1903-cjgpb.

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Proteomic techniques that allow the identification and quantification of stress-related proteins, mapping of dynamics of their expression and posttranslational modifications represent an important approach in the research of plant stresses. In this review, we show an outline of proteomics methods and their applications in the research of plant resistance to various types of stresses.

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Wareth, Gamal, Mathias W. Pletz, Heinrich Neubauer, and Jayaseelan Murugaiyan. "Proteomics of Brucella: Technologies and Their Applications for Basic Research and Medical Microbiology." Microorganisms 8, no. 5 (2020): 766. http://dx.doi.org/10.3390/microorganisms8050766.

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Brucellosis is a global zoonosis caused by Gram-negative, facultative intracellular bacteria of the genus Brucella (B.). Proteomics has been used to investigate a few B. melitensis and B. abortus strains, but data for other species and biovars are limited. Hence, a comprehensive analysis of proteomes will significantly contribute to understanding the enigmatic biology of brucellae. For direct identification and typing of Brucella, matrix-assisted laser desorption ionization—time of flight mass spectrometry (MALDI—TOF MS) has become a reliable tool for routine diagnosis due to its ease of handl

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Saei, Amir Ata, Pierre Sabatier, Ülkü Güler Tokat, Alexey Chernobrovkin, Mohammad Pirmoradian, and Roman A. Zubarev. "Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions." Molecular & Cellular Proteomics 17, no. 6 (2018): 1144–55. http://dx.doi.org/10.1074/mcp.ra118.000610.

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Chemotherapeutics cause the detachment and death of adherent cancer cells. When studying the proteome changes to determine the protein target and mechanism of action of anticancer drugs, the still-attached cells are normally used, whereas the detached cells are usually ignored. To test the hypothesis that proteomes of detached cells contain valuable information, we separately analyzed the proteomes of detached and attached HCT-116, A375, and RKO cells treated for 48 h with 5-fluorouracil, methotrexate and paclitaxel. Individually, the proteomic data on attached and detached cells had comparabl

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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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Kruse, Rikke, Navid Sahebekhtiari, and Kurt Højlund. "The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance." International Journal of Molecular Sciences 21, no. 15 (2020): 5374. http://dx.doi.org/10.3390/ijms21155374.

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Introduction: Mitochondria are essential in energy metabolism and cellular survival, and there is growing evidence that insulin resistance in chronic metabolic disorders, such as obesity, type 2 diabetes (T2D), and aging, is linked to mitochondrial dysfunction in skeletal muscle. Protein profiling by proteomics is a powerful tool to investigate mechanisms underlying complex disorders. However, despite significant advances in proteomics within the past two decades, the technologies have not yet been fully exploited in the field of skeletal muscle proteome. Area covered: Here, we review the curr

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Gao, Xing-Huang, Ling Li, Marc Parisien, et al. "Discovery of a Redox Thiol Switch: Implications for Cellular Energy Metabolism." Molecular & Cellular Proteomics 19, no. 5 (2020): 852–70. http://dx.doi.org/10.1074/mcp.ra119.001910.

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The redox-based modifications of cysteine residues in proteins regulate their function in many biological processes. The gas molecule H2S has been shown to persulfidate redox sensitive cysteine residues resulting in an H2S-modified proteome known as the sulfhydrome. Tandem Mass Tags (TMT) multiplexing strategies for large-scale proteomic analyses have become increasingly prevalent in detecting cysteine modifications. Here we developed a TMT-based proteomics approach for selectively trapping and tagging cysteine persulfides in the cellular proteomes. We revealed the natural protein sulfhydrome

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Mischak, Harald, Eric Schiffer, Petra Zürbig, Mohammed Dakna, and Jochen Metzger. "Urinary Proteome Analysis using Capillary Electrophoresis Coupled to Mass Spectrometry: A Powerful Tool in Clinical Diagnosis, Prognosis and Therapy Evaluation." Journal of Medical Biochemistry 28, no. 4 (2009): 223–34. http://dx.doi.org/10.2478/v10011-009-0020-0.

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Urinary Proteome Analysis using Capillary Electrophoresis Coupled to Mass Spectrometry: A Powerful Tool in Clinical Diagnosis, Prognosis and Therapy EvaluationProteome analysis has emerged as a powerful tool to decipher (patho) physiological processes, resulting in the establishment of the field of clinical proteomics. One of the main goals is to discover biomarkers for diseases from tissues and body fluids. Due to the enormous complexity of the proteome, a separation step is required for mass spectrometry (MS)-based proteome analysis. In this review, the advantages and limitations of protein

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Vowinckel, Jakob, Thomas Corwin, Jonathan Woodsmith, et al. "Proteome and phospho-proteome profiling for deeper phenotype characterization of colorectal cancer heterogeneity." Journal of Clinical Oncology 39, no. 15_suppl (2021): e15536-e15536. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e15536.

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e15536 Background: The rise of precision oncology therapeutics requires deep understanding of the molecular mechanisms implicated in cancer biology. Colorectal cancer (CRC) is one of the first solid tumors to be molecularly characterized by defined genes and pathways. Advances in tumor profiling have revealed a profound molecular heterogeneity in CRC leading to the definition of several consensus molecular subtypes (CMS). However, this molecular heterogeneity is still largely defined on the genomic and transcriptomics level. To complement the understanding of genetically defined molecular subg

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Pitteri, Sharon, and Sam Hanash. "A Systems Approach to the Proteomic Identification of Novel Cancer Biomarkers." Disease Markers 28, no. 4 (2010): 233–39. http://dx.doi.org/10.1155/2010/270859.

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The proteomics field has experienced rapid growth with technologies achieving ever increasing accuracy, sensitivity, and throughput, and with availability of computational tools to address particular applications. Given that the proteome represents the most functional component encoded for in the genome, a systems approach to disease investigations and biomarker identification benefits substantially from integration of proteome level studies. Here we present proteomic approaches that have allowed systematic searches for potential cancer markers by integrating cancer cell profiling with additio

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Eligini, Sonia, Erica Gianazza, Alice Mallia, Stefania Ghilardi, and Cristina Banfi. "Macrophage Phenotyping in Atherosclerosis by Proteomics." International Journal of Molecular Sciences 24, no. 3 (2023): 2613. http://dx.doi.org/10.3390/ijms24032613.

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Macrophages are heterogeneous and plastic cells, able to adapt their phenotype and functions to changes in the microenvironment. They are involved in several homeostatic processes and also in many human diseases, including atherosclerosis, where they participate in all the stages of the disease. For these reasons, macrophages have been studied extensively using different approaches, including proteomics. Proteomics, indeed, may be a powerful tool to better understand the behavior of these cells, and a careful analysis of the proteome of different macrophage phenotypes can help to better charac

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Peck Justice, Sarah A., Monica P. Barron, Guihong D. Qi, et al. "Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome." Journal of Biological Chemistry 295, no. 48 (2020): 16219–38. http://dx.doi.org/10.1074/jbc.ra120.014576.

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Temperature-sensitive (TS) missense mutants have been foundational for characterization of essential gene function. However, an unbiased approach for analysis of biochemical and biophysical changes in TS missense mutants within the context of their functional proteomes is lacking. We applied MS-based thermal proteome profiling (TPP) to investigate the proteome-wide effects of missense mutations in an application that we refer to as mutant thermal proteome profiling (mTPP). This study characterized global impacts of temperature sensitivity–inducing missense mutations in two different subunits o

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Hohn, Andreas, Ivan Iovino, Fabrizio Cirillo, et al. "Bioinformatical Analysis of Organ-Related (Heart, Brain, Liver, and Kidney) and Serum Proteomic Data to Identify Protein Regulation Patterns and Potential Sepsis Biomarkers." BioMed Research International 2018 (March 21, 2018): 1–11. http://dx.doi.org/10.1155/2018/3576157.

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During the last years, proteomic studies have revealed several interesting findings in experimental sepsis models and septic patients. However, most studies investigated protein alterations only in single organs or in whole blood. To identify possible sepsis biomarkers and to evaluate the relationship between protein alteration in sepsis affected organs and blood, proteomics data from the heart, brain, liver, kidney, and serum were analysed. Using functional network analyses in combination with hierarchical cluster analysis, we found that protein regulation patterns in organ tissues as well as

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Chalmel, Frédéric, and Antoine D. Rolland. "Linking transcriptomics and proteomics in spermatogenesis." REPRODUCTION 150, no. 5 (2015): R149—R157. http://dx.doi.org/10.1530/rep-15-0073.

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Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testis-specific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation du

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Nguyen, Nam H. K., Huiyun Wu, Haiyan Tan, et al. "Global Proteomic Profiling of Pediatric AML: A Pilot Study." Cancers 13, no. 13 (2021): 3161. http://dx.doi.org/10.3390/cancers13133161.

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Acute Myeloid Leukemia (AML) is a heterogeneous disease with several recurrent cytogenetic abnormalities. Despite genomics and transcriptomics profiling efforts to understand AML’s heterogeneity, studies focused on the proteomic profiles associated with pediatric AML cytogenetic features remain limited. Furthermore, the majority of biological functions within cells are operated by proteins (i.e., enzymes) and most drugs target the proteome rather than the genome or transcriptome, thus, highlighting the significance of studying proteomics. Here, we present our results from a pilot study investi

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