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Pathologie (Heidelberg, Germany) Dec 2023Proteomics, the study of proteins and their functions, has greatly evolved due to advances in analytical chemistry and computational biology. Unlike genomics or... (Review)
Review
Proteomics, the study of proteins and their functions, has greatly evolved due to advances in analytical chemistry and computational biology. Unlike genomics or transcriptomics, proteomics captures the dynamic and diverse nature of proteins, which play crucial roles in cellular processes. This is exemplified in cancer, where genomic and transcriptomic information often falls short in reflecting actual protein expression and interactions. Liquid chromatography-mass spectrometry (LC-MS) is pivotal in proteomic data generation, enabling high-throughput analysis of protein samples. The MS-based workflow involves protein digestion, chromatographic separation, ionization, and fragmentation, leading to peptide identification and quantification. Computational biostatistics, particularly using tools in R (R Foundation for Statistical Computing, Vienna, Austria; www.R-project.org ), aid in data analysis, revealing protein expression patterns and correlations with clinical variables. Proteomic studies can be explorative, aiming to characterize entire proteomes, or targeted, focusing on specific proteins of interest. The integration of proteomics with genomics addresses database limitations and enhances peptide identification. Case studies in intrahepatic cholangiocarcinoma, glioblastoma multiforme, and pancreatic ductal adenocarcinoma highlight proteomics' clinical applications, from subtyping cancers to identifying diagnostic markers. Moreover, proteomic data augment molecular tumor boards by providing deeper insights into pathway activities and genomic mutations, supporting personalized treatment decisions. Overall, proteomics contributes significantly to advancing our understanding of cellular biology and improving clinical care.
Topics: Humans; Proteomics; Proteome; Peptides; Neoplasms; Computational Biology
PubMed: 37999758
DOI: 10.1007/s00292-023-01261-x -
Proteomics Dec 2022As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal... (Review)
Review
As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.
Topics: Proteomics; Phosphorylation; Glycosylation; Proteome; Protein Processing, Post-Translational
PubMed: 36100958
DOI: 10.1002/pmic.202200070 -
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 -
Nature Methods Feb 2021
Topics: Proteome; Proteomics
PubMed: 33542505
DOI: 10.1038/s41592-021-01069-8 -
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 -
Biochemistry. Biokhimiia Sep 2022Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a... (Review)
Review
Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a proteome scale and mapping the signaling and/or metabolic pathways activated and regulated by these interactions. The methods of chemical proteomics allow not only identifying proteins targeted by drugs, characterizing their toxicity and discovering possible off-target proteins, but also elucidation of the fundamental mechanisms of cell functioning under conditions of drug exposure or due to the changes in physiological state of the organism itself. Solving these problems is essential for both basic research in biology and clinical practice, including approaches to early diagnosis of various forms of serious diseases or prediction of the effectiveness of therapeutic treatment. At the same time, recent developments in high-resolution mass spectrometry have provided the technology for searching the drug targets across the whole cell proteomes. This review provides a concise description of the main objectives and problems of mass spectrometry-based chemical proteomics, the methods and approaches to their solution, and examples of implementation of these methods in biomedical research.
Topics: Drug Delivery Systems; Drug Discovery; Mass Spectrometry; Proteome; Proteomics
PubMed: 36180990
DOI: 10.1134/S0006297922090103 -
Current Pharmaceutical Design 2023Cancer is an ailment with having a very low survival rate globally. Poor cancer prognosis is primarily caused by the fact that people are found to have the disease when... (Review)
Review
BACKGROUND
Cancer is an ailment with having a very low survival rate globally. Poor cancer prognosis is primarily caused by the fact that people are found to have the disease when it is already well advanced. The goal of this study is to compile information on new avenues of investigation into biomarkers that may facilitate the routine detection of cancer. Proteomic analysis has recently developed into a crucial technique for cancer biology research, working in tandem with genomic analysis. Mass spectrometry techniques are one of several proteome analysis techniques that allow for the highly precise quantitative and qualitative recognition of hundreds of proteins in small quantities from various biological materials. These findings might soon serve as the foundation for better cancer diagnostic techniques.
METHODS
An exhaustive literature survey has been conducted using electronic databases such as Google Scholar, Science Direct, and PubMed with keywords of proteomics, applications of proteomics, the technology of proteomics, biomarkers, and patents related to biomarkers.
RESULT
Studies reported till 2021 focusing on cancer proteomics and the related patents have been included in the present review to obtain concrete findings, highlighting the applications of proteomics in cancer.
CONCLUSION
The present review aims to present the overview and insights into cancer proteomics, recent breakthroughs in proteomics techniques, and applications of proteomics with technological advancements, ranging from searching biomarkers to the characterization of molecular pathways, though the entire process is still in its infancy.
Topics: Humans; Proteomics; Biomarkers; Proteome; Neoplasms; Mass Spectrometry
PubMed: 36927422
DOI: 10.2174/1381612829666230316110932 -
Current Opinion in Chemical Biology Feb 2020Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and... (Review)
Review
Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and metabolome of many organisms being readily available, researchers now have the opportunity to dissect how key metabolites regulate complex cellular pathways in vivo. Nonetheless, characterizing the specific and functional protein targets of key metabolites associated with specific cellular phenotypes remains a major challenge. Innovations in chemical biology are now poised to address this fundamental limitation in physiology and disease. In this review, we highlight recent advances in chemoproteomics for targeted and proteome-wide analysis of metabolite-protein interactions that have enabled the discovery of unpredicted metabolite-protein interactions and facilitated the development of new small molecule therapeutics.
Topics: Humans; Metabolome; Metabolomics; Proteins; Proteome; Proteomics
PubMed: 31790852
DOI: 10.1016/j.cbpa.2019.10.008 -
Methods in Molecular Biology (Clifton,... 2023The plasma and serum proteome has enormous potential as a tool for understanding the health of a number of physiological systems. Despite this potential, the use of...
The plasma and serum proteome has enormous potential as a tool for understanding the health of a number of physiological systems. Despite this potential, the use of plasma and serum proteomics clinically and for research is limited, and there are no strict guidelines on how samples should be collected and prepared for proteomic analysis. Given the sensitivity of proteomic analysis, there are a number of pre-analytical variables that should be considered and determined prior to undertaking proteomics-based methodologies.In this chapter, we provide an example of a blood processing protocol and highlight major considerations for pre-analytical variables involving the collection, processing, and handling of blood samples for plasma and serum proteomics. We provide comprehensive notes on aspects of the protocol that must be considered before commencing sample collections for a proteomic study as well as a thorough checklist to be used when designing new proteomic studies.
Topics: Proteomics; Plasma; Specimen Handling; Serum; Proteome
PubMed: 36781777
DOI: 10.1007/978-1-0716-2978-9_3 -
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