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Journal of Neurochemistry Nov 2019This Preface introduces the articles of the special issue on 'Proteomics' where we survey these powerful techniques specifically in the context of applications in...
This Preface introduces the articles of the special issue on 'Proteomics' where we survey these powerful techniques specifically in the context of applications in neurosciences. Proteomics as used here is a catch-all term for approaches where a broad survey of all protein content of a cell or tissue is performed in parallel. In the special issue, various experts outline applications as diverse as finding disease biomarkers in human samples, including living participants or post-mortem brain, as well as application of protein technologies to model systems such as animals and cells. Collectively, these articles outline the utility of current technologies for proteome interrogation and identify enhancements that will shape applications to future studies. This is the Preface for the special issue "Proteomics". Cover Image for this issue: doi: 10.1111/jnc.14530.
Topics: Brain; Humans; Neurosciences; Proteome; Proteomics
PubMed: 31625157
DOI: 10.1111/jnc.14867 -
PloS One 2022Cyanobacteria are prokaryotic Gram-negative organisms prevalent in nearly all habitats. A detailed proteomics study of Cyanobacteria has not been conducted despite...
Cyanobacteria are prokaryotic Gram-negative organisms prevalent in nearly all habitats. A detailed proteomics study of Cyanobacteria has not been conducted despite extensive study of their genome sequences. Therefore, we conducted a proteome-wide analysis of the Cyanobacteria proteome and found Calothrix desertica as the largest (680331.825 kDa) and Candidatus synechococcus spongiarum as the smallest (42726.77 kDa) proteome of the cyanobacterial kingdom. A Cyanobacterial proteome encodes 312.018 amino acids per protein, with a molecular weight of 182173.1324 kDa per proteome. The isoelectric point (pI) of the Cyanobacterial proteome ranges from 2.13 to 13.32. It was found that the Cyanobacterial proteome encodes a greater number of acidic-pI proteins, and their average pI is 6.437. The proteins with higher pI are likely to contain repetitive amino acids. A virtual 2D map of Cyanobacterial proteome showed a bimodal distribution of molecular weight and pI. Several proteins within the Cyanobacterial proteome were found to encode Selenocysteine (Sec) amino acid, while Pyrrolysine amino acids were not detected. The study can enable us to generate a high-resolution cell map to monitor proteomic dynamics. Through this computational analysis, we can gain a better understanding of the bias in codon usage by analyzing the amino acid composition of the Cyanobacterial proteome.
Topics: Isoelectric Point; Proteome; Proteomics; Selenocysteine; Synechococcus
PubMed: 36190972
DOI: 10.1371/journal.pone.0275148 -
Nature Communications Apr 2023Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic...
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.
Topics: Male; Humans; Proteome; Workflow; Peptides; Lung Neoplasms; Proteomics
PubMed: 37012232
DOI: 10.1038/s41467-023-37547-0 -
Circulation Research Jan 2022Rapidly changing and transient protein-protein interactions regulate dynamic cellular processes in the cardiovascular system. Traditional methods, including affinity... (Review)
Review
Rapidly changing and transient protein-protein interactions regulate dynamic cellular processes in the cardiovascular system. Traditional methods, including affinity purification and mass spectrometry, have revealed many macromolecular complexes in cardiomyocytes and the vasculature. Yet these methods often fail to identify in vivo or transient protein-protein interactions. To capture these interactions in living cells and animals with subsequent mass spectrometry identification, enzyme-catalyzed proximity labeling techniques have been developed in the past decade. Although the application of this methodology to cardiovascular research is still in its infancy, the field is developing rapidly, and the promise is substantial. In this review, we outline important concepts and discuss how proximity proteomics has been applied to study physiological and pathophysiological processes relevant to the cardiovascular system.
Topics: Animals; Humans; Myocardium; Protein Interaction Mapping; Protein Interaction Maps; Proteome; Proteomics
PubMed: 35050691
DOI: 10.1161/CIRCRESAHA.121.319810 -
Biochimica Et Biophysica Acta. Proteins... Jul 2021Single-cell analysis came to change the way we look at cell populations. RNA sequencing of single cells allowed us to appreciate the diversity of cell types in the human... (Review)
Review
Single-cell analysis came to change the way we look at cell populations. RNA sequencing of single cells allowed us to appreciate the diversity of cell types in the human brain in an unprecedented manner and its power to reveal cell-type specific changes in cell populations has just begun to be explored. In this context, looking at the proteome of single cells promises to bring functional information and contribute to completing the picture. The potential of single cell proteome, in developing a better understanding of the intricate connections between the very diverse cell populations in the brain, is huge. Whereas early approaches to address single-cell proteome have identified hundreds of proteins, today, techniques combining isobaric labelling and LC-MS can lead to the identification of thousands of proteins. In this review, we describe methods which have been used to identify and quantify proteins from single cells and propose that the application of isobaric labeling and label-free quantitative proteomics approach for single-cell analysis is ready to provide useful information for the neurobiology field.
Topics: Animals; Chromatography, Liquid; Humans; Neurobiology; Proteome; Proteomics; Single-Cell Analysis; Tandem Mass Spectrometry
PubMed: 33845200
DOI: 10.1016/j.bbapap.2021.140658 -
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 -
Expert Review of Proteomics Feb 2021The goal of this review is to highlight the triumphs and frontiers in measurement of the lens proteome as it relates to onset of age-related nuclear cataract. As global... (Review)
Review
INTRODUCTION
The goal of this review is to highlight the triumphs and frontiers in measurement of the lens proteome as it relates to onset of age-related nuclear cataract. As global life expectancy increases, so too does the frequency of age-related nuclear cataracts. Molecular therapeutics do not exist for delay or relief of cataract onset in humans. Since lens fiber cells are incapable of protein synthesis after initial maturation, age-related changes in proteome composition and post-translational modification accumulation can be measured with various techniques. Several of these modifications have been associated with cataract onset.
AREAS COVERED
We discuss the impact of long-lived proteins on the lens proteome and lens homeostasis as well as proteomic techniques that may be used to measure proteomes at various levels of proteomic specificity and spatial resolution.
EXPERT OPINION
There is clear evidence that several proteome modifications are correlated with cataract formation. Past studies should be enhanced with cutting-edge, spatially resolved mass spectrometry techniques to enhance the specificity and sensitivity of modification detection as it relates to cataract formation.
Topics: Cataract; Humans; Lens, Crystalline; Mass Spectrometry; Proteome; Proteomics
PubMed: 33849365
DOI: 10.1080/14789450.2021.1913062 -
Molecules (Basel, Switzerland) Jun 2021Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes... (Review)
Review
Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation and characterization of the milk proteome, such as two-dimensional gel electrophoresis (2DE) technology and especially mass spectrometry (MS) have allowed an exhaustive characterization of the proteins and peptides present in milk and dairy products with enormous applications in the industry for the control of fundamental parameters, such as microbiological safety, the guarantee of authenticity, or the control of the transformations carried out, aimed to increase the quality of the final product.
Topics: Animals; Dairy Products; Electrophoresis, Gel, Two-Dimensional; Female; Mass Spectrometry; Mastitis; Milk; Milk Proteins; Peptides; Protein Processing, Post-Translational; Proteome; Proteomics; Quality Control
PubMed: 34201770
DOI: 10.3390/molecules26133832 -
Molecular & Cellular Proteomics : MCP Apr 2020
Topics: Inventions; Periodicals as Topic; Proteome; Proteomics
PubMed: 32184224
DOI: 10.1074/mcp.E120.002042 -
Platelets Dec 2023Proteomics tools provide a powerful means to identify, detect, and quantify protein-related details in studies of platelet phenotype and function. Here, we consider how...
Proteomics tools provide a powerful means to identify, detect, and quantify protein-related details in studies of platelet phenotype and function. Here, we consider how historical and recent advances in proteomics approaches have informed our understanding of platelet biology, and, how proteomics tools can be used going forward to advance studies of platelets. It is now apparent that the platelet proteome is comprised of thousands of different proteins, where specific changes in platelet protein systems can accompany alterations in platelet function in health and disease. Going forward, many challenges remain in how to best carry out, validate and interpret platelet proteomics experiments. Future studies of platelet protein post-translational modifications such as glycosylation, or studies that take advantage of single cell proteomics and top-down proteomics methods all represent areas of interest to profiling and more richly understanding platelets in human wellness and disease.
Topics: Humans; Blood Platelets; Proteomics; Phenotype; Proteome
PubMed: 37246523
DOI: 10.1080/09537104.2023.2217932