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Expert Review of Proteomics Jan 2021: Proteomic profiling plays an important role in the exploration of cancer from molecular mechanisms to clinical diagnosis and treatment. In recent years, the advent of... (Review)
Review
: Proteomic profiling plays an important role in the exploration of cancer from molecular mechanisms to clinical diagnosis and treatment. In recent years, the advent of new technologies has promoted oncoproteomics from the initial global style to a refined single-cell level.: Among them, the development of microfluidic devices, the improvement of liquid mass spectrometry in accuracy and trace sample handling processes, and the emergence of protein sequencing have contributed to the oncoproteomic analysis at the single-cell level.: The proteomic analysis at the global level and the single-cell level gives different perspectives while combining them can reveal more comprehensive oncoproteomics and help cancer research and treatment strategies.
Topics: Humans; Mass Spectrometry; Neoplasms; Proteome; Proteomics; Single-Cell Analysis
PubMed: 33571016
DOI: 10.1080/14789450.2021.1890036 -
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 -
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 -
Expert Review of Proteomics Feb 2019Acetylation is a widely occurring post-translational modification (PTM) of proteins that plays a crucial role in many cellular physiological and pathological processes.... (Review)
Review
Acetylation is a widely occurring post-translational modification (PTM) of proteins that plays a crucial role in many cellular physiological and pathological processes. Over the last decade, acetylation analyses required the development of multiple methods to target individual acetylated proteins, as well as to cover a broader description of acetylated proteins that comprise the acetylome. Areas covered: This review discusses the different types of acetylation (N-ter/K-/O-acetylation) and then describes some major strategies that have been reported in the literature to detect, enrich, identify and quantify protein acetylation. The review highlights the advantages and limitations of these strategies, to guide researchers in designing their experimental investigations and analysis of protein acetylation. Finally, this review highlights the main applications of acetylomics (proteomics based on mass spectrometry) for understanding physiological and pathological conditions. Expert opinion: Recent advances in acetylomics have enhanced knowledge of the biological and pathological roles of protein acetylation and the acetylome. Besides, radiolabeling and western blotting remain also techniques-of-choice for targeted protein acetylation. Future challenges in acetylomics to analyze the N-ter and K-acetylome will most likely require enrichment/fractionation, MS instrumentation and bioinformatics. Challenges also remain to identify the potential biological roles of O-acetylation and cross-talk with other PTMs.
Topics: Acetylation; Mass Spectrometry; Protein Processing, Post-Translational; Proteome; Proteomics
PubMed: 30580641
DOI: 10.1080/14789450.2019.1559061 -
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 -
Proteomics. Clinical Applications Apr 2016Oncoproteomics is the study of cancer-associated proteins and their interactions using proteomic technologies. It is expected to play a crucial role in the detection and... (Review)
Review
Oncoproteomics is the study of cancer-associated proteins and their interactions using proteomic technologies. It is expected to play a crucial role in the detection and surveillance of cancer, as well as in the development of personalized medicine for oncology. In this review, we will outline the current status, advantages, and limitations of oncoproteomics. Further, we will discuss available strategies arising from a better understanding of oncoproteomics, including integrated omics approaches, to overcome current problems in the discovery and validation of biomarkers, identification of novel drug targets, and management of personalized medicine.
Topics: Biomarkers, Tumor; Gene Expression; Gene Expression Profiling; Humans; Molecular Targeted Therapy; Neoplasm Proteins; Neoplasms; Precision Medicine; Proteome; Proteomics; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tissue Array Analysis
PubMed: 26518147
DOI: 10.1002/prca.201500081 -
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 -
Proteomics Feb 2015The highly complex and species-selective mechanism of fertilization is a central theme of developmental biology. Gametogenesis, sperm activation, and egg-sperm... (Review)
Review
The highly complex and species-selective mechanism of fertilization is a central theme of developmental biology. Gametogenesis, sperm activation, and egg-sperm recognition are fundamental biological processes, warranting detailed studies into the molecular composition of gametes. Biological MS has been instrumental for the comprehensive itemizing of gamete proteomes. The protein constellation of sperm cells and its subcellular structures has been established for a variety of animal species. Spermatogenesis and the crucial activation of sperm cells as a prerequisite of successful fertilization and physiological adaptations to external stressors was investigated using proteomics, as well as the underlying mechanisms of male infertility with respect to proteome-wide alterations. This review outlines recent achievements of sperm proteomics and exemplifies the usefulness of gel-based surveys by outlining the comparative analysis of abnormal spermatozoa in globozoospermia. Besides label-free MS techniques and cell-based labeling methodology, high-resolution fluorescence 2DE has been shown to be highly suitable as a proteomic biomarker discovery tool in sperm protein research. The appropriateness of novel protein markers for improving our understanding of normal spermatogenesis and sperm activation versus the molecular pathogenesis of male infertility will be discussed. New biomarker candidates might be useful to improve diagnostic, prognostic, and therapeutic aspects of infertility.
Topics: Animals; Humans; Male; Proteome; Proteomics; Spermatogenesis; Spermatozoa
PubMed: 24909132
DOI: 10.1002/pmic.201400032 -
Nature Methods Feb 2021
Topics: Proteome; Proteomics
PubMed: 33542505
DOI: 10.1038/s41592-021-01069-8 -
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