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Proteomics characterization of purified SARS-CoV-2 viral particles for search of mutations.

ABSTRACT: Shotgun proteomics characterization of purified SARS-CoV-2 viral particles and interpretation in error-tolerant mode.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean Armengaud

PROVIDER: PXD025130 | Pride | 2021-05-31

REPOSITORIES: Pride

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			Action	DRS
	F217666.dat	Other
	F217666.mzid.gz	Mzid
	F217667.dat	Other
	F217667.mzid.gz	Mzid
	F217668.dat	Other

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Publications

Heterogeneity of SARS-CoV-2 virus produced in cell culture revealed by shotgun proteomics and supported by genome sequencing.

Gallais Fabrice F Pible Olivier O Gaillard Jean-Charles JC Debroas Stéphanie S Batina Hélène H Ruat Sylvie S Sandron Florian F Delafoy Damien D Gerber Zuzana Z Olaso Robert R Gas Fabienne F Bellanger Laurent L Deleuze Jean-François JF Grenga Lucia L Armengaud Jean J

Analytical and bioanalytical chemistry 20210520 29

COVID-19 is the most disturbing pandemic of the past hundred years. Its causative agent, the SARS-CoV-2 virus, has been the subject of an unprecedented investigation to characterize its molecular structure and intimate functioning. While markers for its detection have been proposed and several diagnostic methodologies developed, its propensity to evolve and evade diagnostic tools and the immune response is of great concern. The recent spread of new variants with increased infectivity requires ev ...[more]

PMID: 34013402

Similar Datasets

Proteomics characterization of purified SARS-CoV-2 viral particles.

Project description:Shotgun proteomics characterization of purified SARS-CoV-2 viral particles.

2021-05-31 | PXD025131 | Pride

Proteogenomics analysis of the digestive gland from the mussel Mytilus galloprovincialis exposed to carbamazepine

Project description:teogenomics analysis from digestive glands from Mytilus galloprovincialis exposed to two concentrations of carbamazepine.

2022-04-23 | PXD024201 | Pride

Insights into the digestive gland of Mytilus coruscus under heat stress using TMT-based proteomics

Project description:A healthy existence relationship between mussels and environment relies on suitable PH, adequate oxygen and suitable temperature. Besides ocean acidification, ocean warming has been shown to cause mussel dead, a phenomenon responsible for extensive mussel dead around the word. How heat stress impacts mussel alive is poorly understood. We founded that. The superoxide dismutase (SOD) activity of two treatment groups were significantly higher than that of control group, and the activity of acid phosphatase (ACP) was significantly higher in two treatment groups than control group. The lactate dehydrogenase (LDH) activity of 26 ℃ treatment group was significantly higher than that of control group, and the LDH activity of 33 ℃ treatment group was significantly lower than that of control group. Cellular content of lysozyme (LZM) was significantly higher in two treatment groups than control group. In this study, we applied TMT quantification to investigate how Mytilus coruscus responds to heat stress (26 ℃, 33 ℃). We identified 1652 to 1878 differentially expressed proteins (DEPs) from these heat conditions, among which 897 were commonly regulated by all the two temperature and were significantly enriched in nutrients digestion and absorption (e. g. fat digestion and absorption). Furthermore, proteins associated with nutrients metabolism, signaling pathways (p53 signaling pathway and MAPK signaling pathway)and energy metabolism (e. g. TCA cycle) were impacted, suggesting that the ability of basic metabolism of Mytilus coruscus may be altered by heat stress.

2023-05-30 | PXD035618 | Pride

Proteomic Profiling of Purified Rabies Virus Particles.

Project description:While host proteins incorporated into virions during viral budding from infected cell are known to play essential roles in multiple process of the life cycle of progeny virus, these characteristics have been largely neglected in studies on rabies virus (RABV). Here, we purified the RABV virions with good purity and integrity, and analyzed their proteome by nano LC-MS/MS, followed by the confirmation with immunoblot and immuno-electronic microscopy. In addition to the 5 viral proteins, 49 cellular proteins were reproducibly identified to be incorporated into matured RABV virions. Function annotation suggested that 24 of them were likely involved in virus replication. Furthermore, cryo-EM was employed to observe the purified RABV virions, generating high-resolution pictures of the bullet-shaped virion structure of RABV. This study has provided new insights into the host proteins composition in RABV virion and shed the light for further investigation on molecular mechanisms of RABV infection, as well as the discovery of new anti-RABV therapeutics.

| S-EPMC7090697 | biostudies-literature

Glycosidades of Pomacea canaliculata

Project description:In this study, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was applied to define the occurrence, diversity and origin of glycosyl-hydrolases along the digestive tract of P. canaliculata. Cellulases, hemicellulases, amylases, maltases, fucosidases and galactosidases were identified across the digestive tract. The digestive gland and the contents of the crop and style sac yield a higher diversity of glycosidase-derived peptides.

2019-07-25 | PXD013550 | Pride

ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

Project description:ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

2010-06-25 | E-MTAB-214 | biostudies-arrayexpress

Proteomic analysis of purified Newcastle disease virus particles.

Project description:BackgroundNewcastle disease virus (NDV) is an enveloped RNA virus, bearing severe economic losses to the poultry industry worldwide. Previous virion proteomic studies have shown that enveloped viruses carry multiple host cellular proteins both internally and externally during their life cycle. To address whether it also occurred during NDV infection, we performed a comprehensive proteomic analysis of highly purified NDV La Sota strain particles.ResultsIn addition to five viral structural proteins, we detected thirty cellular proteins associated with purified NDV La Sota particles. The identified cellular proteins comprised several functional categories, including cytoskeleton proteins, annexins, molecular chaperones, chromatin modifying proteins, enzymes-binding proteins, calcium-binding proteins and signal transduction-associated proteins. Among these, three host proteins have not been previously reported in virions of other virus families, including two signal transduction-associated proteins (syntenin and Ras small GTPase) and one tumor-associated protein (tumor protein D52). The presence of five selected cellular proteins (i.e., β-actin, tubulin, annexin A2, heat shock protein Hsp90 and ezrin) associated with the purified NDV particles was validated by Western blot or immunogold labeling assays.ConclusionsThe current study presented the first standard proteomic profile of NDV. The results demonstrated the incorporation of cellular proteins in NDV particles, which provides valuable information for elucidating viral infection and pathogenesis.

| S-EPMC3413529 | biostudies-literature

Proteomic analysis of purified coronavirus infectious bronchitis virus particles.

Project description:BackgroundInfectious bronchitis virus (IBV) is the coronavirus of domestic chickens causing major economic losses to the poultry industry. Because of the complexity of the IBV life cycle and the small number of viral structural proteins, important virus-host relationships likely remain to be discovered. Toward this goal, we performed two-dimensional gel electrophoresis fractionation coupled to mass spectrometry identification approaches to perform a comprehensive proteomic analysis of purified IBV particles.ResultsApart from the virus-encoded structural proteins, we detected 60 host proteins in the purified virions which can be grouped into several functional categories including intracellular trafficking proteins (20%), molecular chaperone (18%), macromolcular biosynthesis proteins (17%), cytoskeletal proteins (15%), signal transport proteins (15%), protein degradation (8%), chromosome associated proteins (2%), ribosomal proteins (2%), and other function proteins (3%). Interestingly, 21 of the total host proteins have not been reported to be present in virions of other virus families, such as major vault protein, TENP protein, ovalbumin, and scavenger receptor protein. Following identification of the host proteins by proteomic methods, the presence of 4 proteins in the purified IBV preparation was verified by western blotting and immunogold labeling detection.ConclusionsThe results present the first standard proteomic profile of IBV and may facilitate the understanding of the pathogenic mechanisms.

| S-EPMC2909931 | biostudies-literature

Polymer type specific microplastic effects on Dreissena bugensis’ proteome, antioxidant activity and behavior

Project description:The freshwater mussel Dreissena bugensis was exposed for nine days to different microplastic particles, in detail, to three petroleum-based polymers (polyamide (PA), polyethylene terephthalate (PET), polystyrene (PS)), to one bio-based polymer (polylactic acid (PLA)) and to ground mussel shells (MS), serving as a natural particle control (size range: 20-75 µm;1000 p ml-1). Behavior endpoints were analyzed with hall sensor based real-time valvometry. Additionally, biochemical alterations of ROS detoxifying enzymes were analyzed, and a proteomic profiling on digestive gland tissue was performed.

2022-11-11 | PXD030056 | Pride

Proteomic analysis of the cardiac relic of Blessed Pauline Jaricot

Project description:Proteomic analysis of the cardiac relic of Blessed Pauline Jaricot upon restoration of the cardiotaph of this 19th century missionary figure. Without any a priori metaproteomics interpretation allowed identification of the proteins and their taxonomical origins.

2023-02-17 | PXD039007 | Pride

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