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Annual Review of Virology Sep 2021The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any... (Review)
Review
The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry-based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time.
Topics: Mass Spectrometry; Proteome; Proteomics; Viral Proteins; Viruses
PubMed: 34129369
DOI: 10.1146/annurev-virology-091919-104458 -
Annual Review of Genomics and Human... Aug 2022Proteins are the molecular effectors of the information encoded in the genome. Proteomics aims at understanding the molecular functions of proteins in their biological... (Review)
Review
Proteins are the molecular effectors of the information encoded in the genome. Proteomics aims at understanding the molecular functions of proteins in their biological context. In contrast to transcriptomics and genomics, the study of proteomes provides deeper insight into the dynamic regulatory layers encoded at the protein level, such as posttranslational modifications, subcellular localization, cell signaling, and protein-protein interactions. Currently, mass spectrometry (MS)-based proteomics is the technology of choice for studying proteomes at a system-wide scale, contributing to clinical biomarker discovery and fundamental molecular biology. MS technologies are continuously being developed to fulfill the requirements of speed, resolution, and quantitative accuracy, enabling the acquisition of comprehensive proteomes. In this review, we present how MS technology and acquisition methods have evolved to meet the requirements of cutting-edge proteomics research, which is describing the human proteome and its dynamic posttranslational modifications with unprecedented depth. Finally, we provide a perspective on studying proteomes at single-cell resolution.
Topics: Genome; Humans; Mass Spectrometry; Protein Processing, Post-Translational; Proteome; Proteomics
PubMed: 35440146
DOI: 10.1146/annurev-genom-112921-024948 -
Proteomics Aug 2022For a long time, targeted and discovery proteomics covered different corners of the detection spectrum, with targeted proteomics focused on small target sets. This... (Review)
Review
For a long time, targeted and discovery proteomics covered different corners of the detection spectrum, with targeted proteomics focused on small target sets. This changed with the recent advances in highly multiplexed analysis. While discovery proteomics still pushes higher numbers of identified and quantified proteins, the advances in targeted proteomics rose to cover large parts of less complex proteomes or proteomes with low protein detection counts due to dynamic range restrictions, like the blood proteome. These new developments will impact, especially on the field of biomarker discovery and the possibility of using targeted proteomics for diagnostic purposes.
Topics: Mass Spectrometry; Proteome; Proteomics
PubMed: 35816345
DOI: 10.1002/pmic.202100330 -
Current Protein & Peptide Science 2021Modern protein science is broadening horizons by moving toward the systemic description of proteins in their natural habitats. This implies a transition from a classical... (Review)
Review
Modern protein science is broadening horizons by moving toward the systemic description of proteins in their natural habitats. This implies a transition from a classical reductionist approach associated with consideration of the unique structure and specific biological activity of an individual protein in a purified form to studying entire proteomes and their functions. This minireview provides a brief description of structural, functional, and expression proteomics, the dark proteome (or unfoldome), and some of the tools utilized in the analyses of proteomes.
Topics: Humans; Proteome; Proteomics
PubMed: 34382522
DOI: 10.2174/1389203722666210812120751 -
Scientific Reports Aug 2020Cancer cells release small extracellular vesicles, exosomes, that have been shown to contribute to various aspects of cancer development and progression. Differential...
Cancer cells release small extracellular vesicles, exosomes, that have been shown to contribute to various aspects of cancer development and progression. Differential analysis of exosomal proteomes from cancerous and non-tumorigenic breast cell lines can provide valuable information related to breast cancer progression and metastasis. Moreover, such a comparison can be explored to find potentially new protein biomarkers for early disease detection. In this study, exosomal proteomes of MDA-MB-231, a metastatic breast cancer cell line, and MCF-10A, a non-cancerous epithelial breast cell line, were identified by nano-liquid chromatography coupled to tandem mass spectrometry. We also tested three exosomes isolation methods (ExoQuick, Ultracentrifugation (UC), and Ultrafiltration-Ultracentrifugation) and detergents (n-dodecyl β-D-maltoside, Triton X-100, and Digitonin) for solubilization of exosomal proteins and enhanced detection by mass spectrometry. A total of 1,107 exosomal proteins were identified in both cell lines, 726 of which were unique to the MDA-MB-231 breast cancer cell line. Among them, 87 proteins were predicted to be relevant to breast cancer and 16 proteins to cancer metastasis. Three exosomal membrane/surface proteins, glucose transporter 1 (GLUT-1), glypican 1 (GPC-1), and disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), were identified as potential breast cancer biomarkers and validated with Western blotting and high-resolution flow cytometry. We demonstrated that exosomes are a rich source of breast cancer-related proteins and surface biomarkers that may be used for disease diagnosis and prognosis.
Topics: Biomarkers, Tumor; Breast Neoplasms; Exosomes; Female; Humans; Mass Spectrometry; Proteome; Proteomics; Tumor Cells, Cultured; Ultracentrifugation
PubMed: 32782317
DOI: 10.1038/s41598-020-70393-4 -
Expert Review of Proteomics 2023Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence... (Review)
Review
INTRODUCTION
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence indicates that dysfunction of glial cells, including astrocytes, microglia, and oligodendrocytes, may contribute to the development and progression of AD. Large-scale analysis of glial proteins sheds light on their roles in cellular processes and diseases. In AD, glial proteomics has been utilized to understand glia-based pathophysiology and identify potential biomarkers and therapeutic targets.
AREA COVERED
In this review, we provide an updated overview of proteomic analysis of glia in the context of AD. Additionally, we discuss current challenges in the field, involving glial complexity and heterogeneity, and describe some cutting-edge proteomic technologies to address them.
EXPERT OPINION
Unbiased comprehensive analysis of glial proteomes aids our understanding of the molecular and cellular mechanisms of AD pathogenesis. These investigations highlight the crucial role of glial cells and provide novel insights into the mechanisms of AD pathology. A deeper understanding of the AD-related glial proteome could offer a repertoire of potential biomarkers and therapeutics. Further technical advancement of glial proteomics will enable us to identify proteins within individual cells and specific cell types, thus significantly enhancing our comprehension of AD pathogenesis.
Topics: Humans; Alzheimer Disease; Proteome; Proteomics; Neuroglia; Biomarkers
PubMed: 37724426
DOI: 10.1080/14789450.2023.2260955 -
Advances in Experimental Medicine and... 2021Proteome analysis of model and non-model plants is a genuine scientific field in expansion. Several technological advances have contributed to the implementation of...
Proteome analysis of model and non-model plants is a genuine scientific field in expansion. Several technological advances have contributed to the implementation of different proteomics approaches for qualitative and quantitative analysis of the dynamics of cellular responses at the protein level. The design of time-resolved experiments and the emergent use of multiplexed proteome analysis using chemical or isotopic and isobaric labeling strategies as well as label-free approaches are generating a vast amount of proteomics data that is going to be essential for analysis of protein posttranslational modifications and implementation of systems biology approaches. Through the target proteomics analysis, especially the ones that combine the untargeted methods, we should expect an improvement in the completeness of the identification of proteome and reveal nuances of regulatory cellular mechanisms related to plant development and responses to environmental stresses. Both genomic sequencing and proteomic advancements in the last decades coupled to integrative data analysis are enriching biological information that was once confined to model plants. Therewith, predictions of a changing environment places proteomics as an especially useful tool for crops performance.
Topics: Plants; Protein Processing, Post-Translational; Proteome; Proteomics; Systems Biology
PubMed: 35113395
DOI: 10.1007/978-3-030-80352-0_3 -
Methods in Molecular Biology (Clifton,... 2022Plasma and serum are rich sources of proteins that are commonly used for clinical proteome profiling and biomarkers discovery. However, high-throughput plasma proteome...
Plasma and serum are rich sources of proteins that are commonly used for clinical proteome profiling and biomarkers discovery. However, high-throughput plasma proteome profiling and quantitative analysis using mass spectrometry are challenging because of the large dynamic range of protein abundance and complexity. To overcome these challenges, we developed a convenient high-throughput workflow of depleted plasma using the 4D-Proteomics feature of the Bruker timsTOF Pro mass spectrometer with data-dependent (PASEF) and data-independent acquisition (diaPASEF) method that can potentially be used in a clinical proteome profiling and biomarker discoveries. This workflow is robust, optimal for high throughput, high proteome depth, and is reproducible. In our sample preparation steps, we used immuno-depletion steps to remove high-abundance plasma proteins, and without any further cleanup steps, we can use depleted plasma samples directly for enzymatic digestion. Immuno-depletion steps and 4D-Proteomics features of timsTOF Pro increase the plasma proteome depth, and accuracy with the identification of >800 protein groups.
Topics: Biomarkers; Blood Proteins; Plasma; Proteome; Proteomics
PubMed: 36127608
DOI: 10.1007/978-1-0716-2565-1_36 -
Advances in Experimental Medicine and... 2021Autophagy is an evolutionarily conserved intracellular degradation process. Autophagy is closely involved in human health and diseases. In recent years, mass...
Autophagy is an evolutionarily conserved intracellular degradation process. Autophagy is closely involved in human health and diseases. In recent years, mass spectrometry-based proteomic methods have become important and powerful tools for autophagy studies. These types of techniques have been especially helpful to reveal the range of degradation substrates of autophagy through large-scale, unbiased analysis of cellular proteomes. At present, a variety of mass spectrometry-based proteomics methods have been successfully applied to autophagy research.
Topics: Autophagy; Humans; Mass Spectrometry; Proteome; Proteomics
PubMed: 34260034
DOI: 10.1007/978-981-16-2830-6_17 -
Biochimica Et Biophysica Acta. Proteins... Nov 2020Saliva is identified as functional equivalent to serum, reflecting the physiological state of the body, as well as hormonal, emotional, nutritional and metabolic... (Review)
Review
Saliva is identified as functional equivalent to serum, reflecting the physiological state of the body, as well as hormonal, emotional, nutritional and metabolic alterations. The application of mass spectrometry based approaches has allowed a thorough characterization of the saliva proteome and led to the discovery of putative biomarkers. Several salivary biomarkers have been recently explored as potentially useful screening tools in patients diagnosed with metabolic disorders. In this review, we provide an overview of saliva proteomics studies, with a focus on diabetes, and we explore the evidence for the utility of well identified markers for the diagnosis and monitoring of the disease. Emerging approaches in salivary diagnostics that may significantly advance the field of diabetes research are also highlighted.
Topics: Biomarkers; Diabetes Mellitus; Humans; Proteome; Proteomics; Saliva
PubMed: 32663525
DOI: 10.1016/j.bbapap.2020.140494