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Journal of Proteomics Feb 2020Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO and HO. It also serves... (Review)
Review
Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO and HO. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30-50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.
Topics: Adaptation, Physiological; Chloroplast Proteins; Chloroplasts; Photosynthesis; Proteome; Proteomics
PubMed: 31704367
DOI: 10.1016/j.jprot.2019.103542 -
Methods in Molecular Biology (Clifton,... 2022Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and...
Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, providing the capabilities of identification and quantitation of thousands of proteins. The technology has been applied to biomarker discovery and understanding the mechanisms of drug action. Both stable isotope labeling of proteins or peptides and label-free approaches have been incorporated with multidimensional LC separation and tandem mass spectrometry (LC-MS/MS) to increase the coverage and depth of proteome analysis. A protocol of such an approach exemplified by dimethyl labeling in combination with 2D-LC-MS/MS is described. With further development of novel proteomic tools and increase in sample throughput, the full spectrum of mass spectrometry-based proteomic research will greatly advance systems medicine.
Topics: Biomarkers; Chromatography, Liquid; Proteome; Proteomics; Tandem Mass Spectrometry
PubMed: 35437715
DOI: 10.1007/978-1-0716-2265-0_1 -
Molecular Omics Mar 2023Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically... (Review)
Review
Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically susceptible to damage from individual types of exposure. Amino acid content is not completely predictive of protein susceptibility, as secondary, tertiary, and quaternary structures of proteins strongly influence the reactivity of the proteome to individual exposures. Because we cannot readily predict which proteins will be affected by which chemical exposures, mass spectrometry-based proteomic strategies are necessary to determine the protein targets of environmental toxins and toxicants. This review describes the mechanisms by which environmental exposure to toxins and toxicants can damage proteins and affect their function, and emerging omic methodologies that can be used to identify the protein targets of a given agent. These methods include target identification strategies that have recently revolutionized the drug discovery field, such as activity-based protein profiling, protein footprinting, and protein stability profiling technologies. In particular, we highlight the necessity of multiple, complementary approaches to fully interrogate how protein integrity is challenged by individual exposures.
Topics: Proteomics; Proteome; Mass Spectrometry
PubMed: 36655925
DOI: 10.1039/d2mo00246a -
Methods in Molecular Biology (Clifton,... 2023Extracellular vesicles (EVs) have emerged as a valuable source for disease biomarkers and an alternative drug delivery system due to their ability to carry cargo and...
Extracellular vesicles (EVs) have emerged as a valuable source for disease biomarkers and an alternative drug delivery system due to their ability to carry cargo and target specific cells. Proper isolation, identification, and analytical strategy are required for evaluating their potential in diagnostics and therapeutics. Here, a method is detailed to isolate plasma EVs and analyze their proteomic profiling, combining EVtrap-based high-recovery EV isolation, phase-transfer surfactant method for protein extraction, and mass spectrometry qualitative and quantitative strategies for EV proteome characterization. The pipeline provides a highly effective EV-based proteome analysis technique that can be applied for EV characterization and evaluation of EV-based diagnosis and therapy.
Topics: Proteome; Proteomics; Extracellular Vesicles; Mass Spectrometry; Biomarkers
PubMed: 37191799
DOI: 10.1007/978-1-0716-3163-8_14 -
Journal of Chemical Information and... Dec 2022Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years,... (Review)
Review
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years, especially the subcellular proteomics. Numerous evidence indicate that the subcellular localization of proteins is associated with various cellular processes and disease progression. Mass spectrometry (MS)-based and imaging-based experimental approaches have been developed to acquire large-scale spatial proteomic data. To allow the reliable analysis of increasingly complex spatial proteomics data, machine learning (ML) methods have been widely used in both MS-based and imaging-based spatial proteomic data analysis pipelines. Here, we comprehensively survey the applications of ML in spatial proteomics from following aspects: (1) data resources for spatial proteome are comprehensively introduced; (2) the roles of different ML algorithms in data analysis pipelines are elaborated; (3) successful applications of spatial proteomics and several analytical tools integrating ML methods are presented; (4) challenges existing in modern ML-based spatial proteomics studies are discussed. This review provides guidelines for researchers seeking to apply ML methods to analyze spatial proteomic data and can facilitate insightful understanding of cell biology as well as the future research in medical and drug discovery communities.
Topics: Proteomics; Proteome; Mass Spectrometry; Machine Learning; Algorithms
PubMed: 36378082
DOI: 10.1021/acs.jcim.2c01161 -
Cells Nov 2023Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably... (Review)
Review
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
Topics: Humans; Proteome; Proteomics; Muscle Fibers, Skeletal; Muscle, Skeletal; Mass Spectrometry
PubMed: 37947638
DOI: 10.3390/cells12212560 -
Nature Methods Feb 2021
Topics: Proteome; Proteomics
PubMed: 33542505
DOI: 10.1038/s41592-021-01069-8 -
Methods in Molecular Biology (Clifton,... 2022Multiplexed enhanced protein dynamic mass spectrometry (mePROD MS) enables robust quantification of translation in cell culture. Tandem mass tags (TMT) are combined with...
Multiplexed enhanced protein dynamic mass spectrometry (mePROD MS) enables robust quantification of translation in cell culture. Tandem mass tags (TMT) are combined with pulsed stable isotope labeling in cell culture (pSILAC) to monitor newly synthesized proteins on a proteome wide scale. While approaches combining pSILAC and TMT typically require long labeling times to reach sufficient intensity of the newly synthesized peptides in the mass spectrometer, mePROD uses a carrier signal that boosts the survey scan intensity and strongly increases identification rates. Hence, this protocol provides an easy and cost-efficient method to profile proteome-wide translatome changes at a temporal resolution of minutes.
Topics: Isotope Labeling; Mass Spectrometry; Peptides; Proteome; Proteomics
PubMed: 35171474
DOI: 10.1007/978-1-0716-1975-9_5 -
Journal of Proteome Research Aug 2022Single-cell proteomics is a promising field to provide direct yet comprehensive molecular insights into cellular functions without averaging effects. Here, we address a... (Review)
Review
Single-cell proteomics is a promising field to provide direct yet comprehensive molecular insights into cellular functions without averaging effects. Here, we address a grand technical challenge impeding the maturation of single-cell proteomics─protein adsorption loss (PAL). Even though widely known, there is currently no quantitation on how profoundly and selectively PAL has affected single-cell proteomics. Therefore, the mitigations to this challenge have been generic, and their efficacy was only evaluated by the size of the resolved proteome with no specificity on individual proteins. We use the existing knowledge of PAL, protein expression, and the typical surface area used in single-cell proteomics to discuss the severity of protein loss. We also summarize the current solutions to this challenge and briefly review the available methods to characterize the physical and chemical properties of protein surface adsorption. By citing successful strategies in single-cell genomics for measurement errors in individual transcripts, we pinpoint the urgency to benchmark PAL at the proteome scale with individual protein resolution. Finally, orthogonal single-cell proteomic techniques that have the potential to cross validate PAL are proposed. We hope these efforts can promote the fruition of single-cell proteomics in the near future.
Topics: Adsorption; Proteome; Proteomics
PubMed: 35849481
DOI: 10.1021/acs.jproteome.2c00317 -
Journal of Basic Microbiology Jun 2020An organism exposed to a plethora of environmental perturbations undergoes proteomic changes which enable the characterization of total proteins in it. Much of the... (Review)
Review
An organism exposed to a plethora of environmental perturbations undergoes proteomic changes which enable the characterization of total proteins in it. Much of the proteomic information is obtained from genomic data. Additional information on the proteome such as posttranslational modifications, protein-protein interactions, protein localization, metabolic pathways, and so on are deduced using proteomic tools which genomics and transcriptomics fail to offer. The proteomic analysis allows identification of precise changes in proteins, which in turn solve the complexity of microbial population providing insights into the microbial metabolism, cellular pathways, and behavior of microorganisms in new environments. Furthermore, they provide clues for the exploitation of their special features for biotechnological applications. Numerous techniques for the analysis of microbial proteome such as electrophoretic, chromatographic, mass spectrometric-based methods as well as quantitative proteomics are available which facilitate protein separation, expression, identification, and quantification of proteins. An understanding of the potential of each of the proteomic tools has created a significant impact on diverse microbiological aspects and the same has been discussed in this review.
Topics: Bacterial Proteins; Microbiological Techniques; Microbiology; Proteome; Proteomics
PubMed: 32212201
DOI: 10.1002/jobm.201900628