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Article ; Online: Profiling SARS-CoV-2 Infection by High-Throughput Shotgun Proteomics.

Grenga, Lucia / Gouveia, Duarte / Armengaud, Jean

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2452, Page(s) 167–182

Abstract: A comprehensive cartography of viral and host proteins expressed during the different stages of SARS-CoV-2 infection is key to decipher the molecular mechanisms of pathogenesis. For the most detailed analysis, proteins should be first purified and then ... ...

Abstract	A comprehensive cartography of viral and host proteins expressed during the different stages of SARS-CoV-2 infection is key to decipher the molecular mechanisms of pathogenesis. For the most detailed analysis, proteins should be first purified and then proteolyzed with trypsin in the presence of detergents. The resulting peptide mixtures are resolved by reverse phase ultrahigh pressure liquid chromatography and then identified by a high-resolution tandem mass spectrometer. The thousands of spectra acquired for each fraction can then be assigned to peptide sequences using a relevant protein sequence database, comprising viral and host proteins and potential contaminants from the growth medium or from the operator. The peptides are evidencing proteins and their intensities are used to infer the abundance of their corresponding proteins. Data analysis allows for highlighting the viral and host proteins dynamics. Here, we describe the sample preparation method adapted to profile SARS-CoV-2 -infected cell models, the shotgun proteomics pipeline to record experimental data, and the workflow for data interpretation to analyze infection-induced proteomic changes in a time-resolved manner.
MeSH term(s)	COVID-19 ; Humans ; Peptides ; Proteomics/methods ; SARS-CoV-2 ; Tandem Mass Spectrometry
Chemical Substances	Peptides
Language	English
Publishing date	2022-05-12
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2111-0_11
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Article ; Online: Proteomics in the COVID-19 Battlefield: First Semester Check-Up.

Grenga, Lucia / Armengaud, Jean

Proteomics

2020 Volume 21, Issue 1, Page(s) e2000198

Abstract: Proteomics offers a wide collection of methodologies to study biological systems at the finest granularity. Faced with COVID-19, the most worrying pandemic in a century, proteomics researchers have made significant progress in understanding how the ... ...

Abstract	Proteomics offers a wide collection of methodologies to study biological systems at the finest granularity. Faced with COVID-19, the most worrying pandemic in a century, proteomics researchers have made significant progress in understanding how the causative virus hijacks the host's cellular machinery and multiplies exponentially, how the disease can be diagnosed, and how it develops, as well as its severity predicted. Numerous cellular targets of potential interest for the development of new antiviral drugs have been documented. Here, the most striking results obtained in the proteomics field over this first semester of the pandemic are presented. The molecular machinery of SARS-CoV-2 is much more complex than initially believed, as many post-translational modifications can occur, leading to a myriad of proteoforms and a broad heterogeneity of viral particles. The interplay of protein-protein interactions, protein abundances, and post-translational modifications has yet to be fully documented to provide a full picture of this intriguing but lethal biological threat. Proteomics has the potential to provide rapid detection of the SARS-CoV-2 virus by mass spectrometry proteotyping, and to further increase the knowledge of severe respiratory syndrome COVID-19 and its long-term health consequences.
MeSH term(s)	Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Humans ; Pandemics ; Protein Interaction Maps ; Proteome/metabolism ; Proteomics/methods ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology ; Tandem Mass Spectrometry/methods ; Viral Proteins/analysis
Chemical Substances	Proteome ; Viral Proteins ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2020-12-02
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202000198
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes.

Dumas, Thibaut / Martinez Pinna, Roxana / Lozano, Clément / Radau, Sonja / Pible, Olivier / Grenga, Lucia / Armengaud, Jean

Microbiome

2024 Volume 12, Issue 1, Page(s) 46

Abstract: Background: By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems.: ...

Abstract	Background: By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems. Results: Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria. Conclusions: Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract.
MeSH term(s)	Humans ; Tandem Mass Spectrometry/methods ; Proteomics/methods ; Peptides ; Microbiota ; Databases, Protein
Chemical Substances	Peptides
Language	English
Publishing date	2024-03-07
Publishing country	England
Document type	Video-Audio Media ; Journal Article
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-024-01766-4
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Article ; Online: Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives.

Hardouin, Pauline / Chiron, Raphael / Marchandin, Hélène / Armengaud, Jean / Grenga, Lucia

Genes

2021 Volume 12, Issue 6

Abstract: Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator ( ...

Abstract	Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (
MeSH term(s)	Animals ; Cystic Fibrosis/metabolism ; Cystic Fibrosis/microbiology ; Host-Pathogen Interactions ; Humans ; Metagenomics/methods ; Microbiota ; Proteome/genetics ; Proteome/metabolism ; Proteomics/methods
Chemical Substances	Proteome
Language	English
Publishing date	2021-06-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060892
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Article: Quick and wide-range taxonomical repertoire establishment of the cystic fibrosis lung microbiota by tandem mass spectrometry on sputum samples.

Hardouin, Pauline / Pible, Olivier / Marchandin, Hélène / Culotta, Karen / Armengaud, Jean / Chiron, Raphaël / Grenga, Lucia

Frontiers in microbiology

2022 Volume 13, Page(s) 975883

Abstract: Microorganisms proteotyping by tandem mass spectrometry has been recently shown as a powerful methodology to identify the wide-range taxonomy and biomass of microbiota. Sputum is the recommended specimen for routine microbiological monitoring of Cystic ... ...

Abstract	Microorganisms proteotyping by tandem mass spectrometry has been recently shown as a powerful methodology to identify the wide-range taxonomy and biomass of microbiota. Sputum is the recommended specimen for routine microbiological monitoring of Cystic Fibrosis (
Language	English
Publishing date	2022-10-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.975883
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Article ; Online: Quick microbial molecular phenotyping by differential shotgun proteomics.

Gouveia, Duarte / Grenga, Lucia / Pible, Olivier / Armengaud, Jean

Environmental microbiology

2020 Volume 22, Issue 8, Page(s) 2996–3004

Abstract: Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied to study (i) specific microorganisms subjected to a variety of growth or stress ... ...

Abstract	Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied to study (i) specific microorganisms subjected to a variety of growth or stress conditions or (ii) different microorganisms sampled in the same condition. In microbiology, this comparison is particularly successful because differing microorganism phenotypes are explained by clearly altered abundances of key protein players. The extensive description and quantification of proteins from any given microorganism can be routinely obtained for several conditions within a few days by tandem mass spectrometry. Such protein-centred microbial molecular phenotyping is rich in information. However, well-designed experimental strategies, carefully parameterized analytical pipelines, and sound statistical approaches must be applied if the shotgun proteomic data are to be correctly interpreted. This minireview describes these key items for a quick molecular phenotyping based on label-free quantification shotgun proteomics.
MeSH term(s)	Archaea/genetics ; Archaea/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Fungi/genetics ; Fungi/metabolism ; Phenotype ; Proteins/analysis ; Proteomics/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Proteins
Language	English
Publishing date	2020-03-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.14975
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Article ; Online: Mass spectrometry detection of monkeypox virus: Comprehensive coverage for ranking the most responsive peptide markers.

Lozano, Clément / Grenga, Lucia / Gallais, Fabrice / Miotello, Guylaine / Bellanger, Laurent / Armengaud, Jean

Proteomics

2022 Volume 23, Issue 2, Page(s) e2200253

Abstract: The recent and sudden outbreak of monkeypox in numerous non-endemic countries requires expanding its surveillance immediately and understanding its origin and spread. As learned from the COVID-19 pandemic, appropriate detection techniques are crucial to ... ...

Abstract	The recent and sudden outbreak of monkeypox in numerous non-endemic countries requires expanding its surveillance immediately and understanding its origin and spread. As learned from the COVID-19 pandemic, appropriate detection techniques are crucial to achieving such a goal. Mass spectrometry has the advantages of a rapid response, low analytical interferences, better precision, and easier multiplexing to detect various pathogens and their variants. In this proteomic dataset, we report experimental data on the proteome of the monkeypox virus (MPXV) recorded by state-of-the-art shotgun proteomics, including data-dependent and data-independent acquisition for comprehensive coverage. We highlighted 152 viral proteins, corresponding to an overall proteome coverage of 79.5 %. Among the 1371 viral peptides detected, 35 peptides with the most intense signals in mass spectrometry were selected, representing a subset of 13 viral proteins. Their relevance as potential candidate markers for virus detection by targeted mass spectrometry is discussed. This report should assist the rapid development of mass spectrometry-based tests to detect a pathogen of increasing concern.
MeSH term(s)	Humans ; Mass Spectrometry/methods ; Monkeypox virus/isolation & purification ; Peptides/analysis ; Proteome ; Proteomics/methods ; Viral Proteins/chemistry ; Mpox (monkeypox)/diagnosis
Chemical Substances	Peptides ; Proteome ; Viral Proteins
Language	English
Publishing date	2022-08-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200253
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Proteomic insights into Helcococcus kunzii in a diabetic foot ulcer-like environment.

Durand, Benjamin A R N / Dunyach-Remy, Catherine / El Kaddouri, Oumayma / Daher, Riham / Lavigne, Jean-Philippe / Armengaud, Jean / Grenga, Lucia

Proteomics. Clinical applications

2023 Volume 17, Issue 4, Page(s) e2200069

Abstract: Purpose: Helcococcus kunzii is a skin commensal, Gram-positive bacterium, mostly isolated from infected chronic wounds. This opportunistic pathogen is usually co-isolated with Staphylococcus aureus. The present dataset explores the production and ... ...

Abstract	Purpose: Helcococcus kunzii is a skin commensal, Gram-positive bacterium, mostly isolated from infected chronic wounds. This opportunistic pathogen is usually co-isolated with Staphylococcus aureus. The present dataset explores the production and secretion of H. kunzii bacterial virulence interacting proteins in a growth medium mimicking chronic wounds in exponential and stationary growth phases. Experimental design: The H. kunzii cellular proteome and exoproteome were assessed by analyzing three biological replicates per condition tested. Samples were analyzed using a Q-Exactive HF mass spectrometer. Comparative and functional analyses were performed to profile the identified protein set. Results: The H. kunzii's cellular proteome encompassed 969 proteins, among which 64 and 53 were specifically identified in the exponential and stationary phase of growth, respectively. Its exoproteome comprised 58 proteins, among which 16 and 14 were characteristic of each growth stage. Metabolic differences between the two phases of growth are discussed. Besides, the production of previously shortlisted and novel putative H. kunzii targets involved in modulating the virulence of S. aureus is investigated. Conclusion and clinical relevance: This work, pioneering the study of H. kunzii physiology in a chronic wound-like environment, should assist future research on this opportunistic pathogen and the search for innovative approaches for wound management.
MeSH term(s)	Humans ; Diabetic Foot ; Proteome/genetics ; Staphylococcus aureus ; Proteomics ; Gram-Positive Cocci ; Diabetes Mellitus
Chemical Substances	Proteome
Language	English
Publishing date	2023-04-27
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2261788-7
ISSN	1862-8354 ; 1862-8346
ISSN (online)	1862-8354
ISSN	1862-8346
DOI	10.1002/prca.202200069
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Article ; Online: Pathogen proteotyping: A rapidly developing application of mass spectrometry to address clinical concerns.

Grenga, Lucia / Pible, Olivier / Armengaud, Jean

Clinical mass spectrometry (Del Mar, Calif.)

2019 Volume 14 Pt A, Page(s) 9–17

Abstract: For the rapid and reliable differentiation of clinically-relevant bacterial species, mass spectrometry-based methods have emerged in recent years as valid alternatives to existing techniques. Mass profiles generated by whole-cell Matrix-Assisted Laser ... ...

Abstract	For the rapid and reliable differentiation of clinically-relevant bacterial species, mass spectrometry-based methods have emerged in recent years as valid alternatives to existing techniques. Mass profiles generated by whole-cell Matrix-Assisted Laser Desorption Ionization-Time of Flight mass spectrometry have revolutionized microorganism identification and proven their potential for proteotyping at the species level. Indeed, the methodology has been widely deployed in clinical settings. However, the low resolution and dynamic range of the methodology has limited its capacity to distinguish between subspecies. This discrimination capacity is pivotal in cases where certain strains display virulence or antibiotic resistance, and for epidemiologic analyses. Moreover, sensitivity and specificity are both key parameters when attempting to discriminate between microorganisms present in complex multi-pathogenic samples. These two parameters are also essential to meet the growing interest in the characterization of microorganisms contained within even more complex samples, such as the human microbiome. Tandem mass spectrometry, with its high resolution, holds great potential for use in the real-time direct analysis of pathogens at the most relevant taxonomic rank in routine clinical practice. This review explores the numerous benefits and challenges of implementing advanced proteotyping methods, based on tandem mass spectrometry, in clinical laboratories. We provide an overview of the current applications and methodologies, while also discussing recent improvements and potential new approaches for typing, as well as their future applications.
Language	English
Publishing date	2019-04-29
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2376-9998
ISSN (online)	2376-9998
DOI	10.1016/j.clinms.2019.04.004
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Article: Mechanisms Leading to Gut Dysbiosis in COVID-19: Current Evidence and Uncertainties Based on Adverse Outcome Pathways.

Clerbaux, Laure-Alix / Fillipovska, Julija / Muñoz, Amalia / Petrillo, Mauro / Coecke, Sandra / Amorim, Maria-Joao / Grenga, Lucia

Journal of clinical medicine

2022 Volume 11, Issue 18

Abstract: Alteration in gut microbiota has been associated with COVID-19. However, the underlying mechanisms remain poorly understood. Here, we outlined three potential interconnected mechanistic pathways leading to gut dysbiosis as an adverse outcome following ... ...

Abstract	Alteration in gut microbiota has been associated with COVID-19. However, the underlying mechanisms remain poorly understood. Here, we outlined three potential interconnected mechanistic pathways leading to gut dysbiosis as an adverse outcome following SARS-CoV-2 presence in the gastrointestinal tract. Evidence from the literature and current uncertainties are reported for each step of the different pathways. One pathway investigates evidence that intestinal infection by SARS-CoV-2 inducing intestinal inflammation alters the gut microbiota. Another pathway links the binding of viral S protein to angiotensin-converting enzyme 2 (ACE2) to the dysregulation of this receptor, essential in intestinal homeostasis-notably for amino acid metabolism-leading to gut dysbiosis. Additionally, SARS-CoV-2 could induce gut dysbiosis by infecting intestinal bacteria. Assessing current evidence within the Adverse Outcome Pathway framework justifies confidence in the proposed mechanisms to support disease management and permits the identification of inconsistencies and knowledge gaps to orient further research.
Language	English
Publishing date	2022-09-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11185400
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