Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data.
Identifieur interne : 000610 ( Main/Exploration ); précédent : 000609; suivant : 000611Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data.
Auteurs : Duarte Gouveia [France] ; Lucia Grenga [France] ; Jean-Charles Gaillard [France] ; Fabrice Gallais [France] ; Laurent Bellanger [France] ; Olivier Pible [France] ; Jean Armengaud [France]Source :
- Proteomics [ 1615-9861 ] ; 2020.
Descripteurs français
- KwdFr :
- Animaux (MeSH), Betacoronavirus (composition chimique), Betacoronavirus (isolement et purification), Cellules Vero (MeSH), Humains (MeSH), Infections à coronavirus (diagnostic), Infections à coronavirus (virologie), Pandémies (MeSH), Peptides (analyse), Pneumopathie virale (diagnostic), Pneumopathie virale (virologie), Protéines virales (analyse), Protéines virales structurales (analyse), Protéomique (MeSH), Spectrométrie de masse en tandem (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- analyse : Peptides, Protéines virales, Protéines virales structurales.
- composition chimique : Betacoronavirus.
- diagnostic : Infections à coronavirus, Pneumopathie virale.
- isolement et purification : Betacoronavirus.
- virologie : Infections à coronavirus, Pneumopathie virale.
- Animaux, Cellules Vero, Humains, Pandémies, Protéomique, Spectrométrie de masse en tandem, Séquence d'acides aminés.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Animals (MeSH), Betacoronavirus (chemistry), Betacoronavirus (isolation & purification), Chlorocebus aethiops (MeSH), Coronavirus Infections (diagnosis), Coronavirus Infections (virology), Humans (MeSH), Pandemics (MeSH), Peptides (analysis), Pneumonia, Viral (diagnosis), Pneumonia, Viral (virology), Proteomics (MeSH), Tandem Mass Spectrometry (MeSH), Vero Cells (MeSH), Viral Proteins (analysis), Viral Structural Proteins (analysis).
- MESH :
- chemical , analysis : Peptides, Viral Proteins, Viral Structural Proteins.
- chemistry : Betacoronavirus.
- diagnosis : Coronavirus Infections, Pneumonia, Viral.
- isolation & purification : Betacoronavirus.
- virology : Coronavirus Infections, Pneumonia, Viral.
- Amino Acid Sequence, Animals, Chlorocebus aethiops, Humans, Pandemics, Proteomics, Tandem Mass Spectrometry, Vero Cells.
Abstract
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data-dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyzed in terms of their analytical characteristics, species specificity and conservation, and their proneness to structural modifications. Based on these results, a shortlist of 14 peptides from the N, S, and M main structural proteins that could be used for targeted mass-spectrometry method development and diagnostic of the new SARS-CoV-2 is proposed and the best candidates are commented.
DOI: 10.1002/pmic.202000107
PubMed: 32462744
PubMed Central: PMC7267140
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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sortKey="Grenga, Lucia" sort="Grenga, Lucia" uniqKey="Grenga L" first="Lucia" last="Grenga">Lucia Grenga</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Gaillard, Jean Charles" sort="Gaillard, Jean Charles" uniqKey="Gaillard J" first="Jean-Charles" last="Gaillard">Jean-Charles Gaillard</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Gallais, Fabrice" sort="Gallais, Fabrice" uniqKey="Gallais F" first="Fabrice" last="Gallais">Fabrice Gallais</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Bellanger, Laurent" sort="Bellanger, Laurent" uniqKey="Bellanger L" first="Laurent" last="Bellanger">Laurent Bellanger</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Pible, Olivier" sort="Pible, Olivier" uniqKey="Pible O" first="Olivier" last="Pible">Olivier Pible</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Armengaud, Jean" sort="Armengaud, Jean" uniqKey="Armengaud J" first="Jean" last="Armengaud">Jean Armengaud</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author></analytic><series><title level="j">Proteomics</title><idno type="eISSN">1615-9861</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Animals (MeSH)</term><term>Betacoronavirus (chemistry)</term><term>Betacoronavirus (isolation & purification)</term><term>Chlorocebus aethiops (MeSH)</term><term>Coronavirus Infections (diagnosis)</term><term>Coronavirus Infections (virology)</term><term>Humans (MeSH)</term><term>Pandemics (MeSH)</term><term>Peptides (analysis)</term><term>Pneumonia, Viral (diagnosis)</term><term>Pneumonia, Viral (virology)</term><term>Proteomics (MeSH)</term><term>Tandem Mass Spectrometry (MeSH)</term><term>Vero Cells (MeSH)</term><term>Viral Proteins (analysis)</term><term>Viral Structural Proteins (analysis)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux (MeSH)</term><term>Betacoronavirus (composition chimique)</term><term>Betacoronavirus (isolement et purification)</term><term>Cellules Vero (MeSH)</term><term>Humains (MeSH)</term><term>Infections à coronavirus (diagnostic)</term><term>Infections à coronavirus (virologie)</term><term>Pandémies (MeSH)</term><term>Peptides (analyse)</term><term>Pneumopathie virale (diagnostic)</term><term>Pneumopathie virale (virologie)</term><term>Protéines virales (analyse)</term><term>Protéines virales structurales (analyse)</term><term>Protéomique (MeSH)</term><term>Spectrométrie de masse en tandem (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Peptides</term><term>Viral Proteins</term><term>Viral Structural Proteins</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Peptides</term><term>Protéines virales</term><term>Protéines virales structurales</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Chlorocebus aethiops</term><term>Humans</term><term>Pandemics</term><term>Proteomics</term><term>Tandem Mass Spectrometry</term><term>Vero Cells</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Cellules Vero</term><term>Humains</term><term>Pandémies</term><term>Protéomique</term><term>Spectrométrie de masse en tandem</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data-dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyzed in terms of their analytical characteristics, species specificity and conservation, and their proneness to structural modifications. Based on these results, a shortlist of 14 peptides from the N, S, and M main structural proteins that could be used for targeted mass-spectrometry method development and diagnostic of the new SARS-CoV-2 is proposed and the best candidates are commented.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32462744</PMID><DateCompleted><Year>2020</Year><Month>07</Month><Day>28</Day></DateCompleted><DateRevised><Year>2020</Year><Month>07</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1615-9861</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>14</Issue><PubDate><Year>2020</Year><Month>07</Month></PubDate></JournalIssue><Title>Proteomics</Title><ISOAbbreviation>Proteomics</ISOAbbreviation></Journal><ArticleTitle>Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data.</ArticleTitle><Pagination><MedlinePgn>e2000107</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/pmic.202000107</ELocationID><Abstract><AbstractText>Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data-dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyzed in terms of their analytical characteristics, species specificity and conservation, and their proneness to structural modifications. Based on these results, a shortlist of 14 peptides from the N, S, and M main structural proteins that could be used for targeted mass-spectrometry method development and diagnostic of the new SARS-CoV-2 is proposed and the best candidates are commented.</AbstractText><CopyrightInformation>© 2020 The Authors. Proteomics published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gouveia</LastName><ForeName>Duarte</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grenga</LastName><ForeName>Lucia</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaillard</LastName><ForeName>Jean-Charles</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gallais</LastName><ForeName>Fabrice</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bellanger</LastName><ForeName>Laurent</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pible</LastName><ForeName>Olivier</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Armengaud</LastName><ForeName>Jean</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0003-1589-445X</Identifier><AffiliationInfo><Affiliation>Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>ANR-17-CE18-0023-01</GrantID><Agency>Agence Nationale de la Recherche</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Proteomics</MedlineTA><NlmUniqueID>101092707</NlmUniqueID><ISSNLinking>1615-9853</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010455">Peptides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015678">Viral Structural Proteins</NameOfSubstance></Chemical></ChemicalList><SupplMeshList><SupplMeshName Type="Disease" UI="C000657245">COVID-19</SupplMeshName><SupplMeshName Type="Organism" UI="C000656484">severe acute respiratory syndrome coronavirus 2</SupplMeshName></SupplMeshList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002522" MajorTopicYN="N">Chlorocebus aethiops</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="N">diagnosis</QualifierName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010455" MajorTopicYN="N">Peptides</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="N">diagnosis</QualifierName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040901" MajorTopicYN="N">Proteomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053719" MajorTopicYN="N">Tandem Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014709" MajorTopicYN="N">Vero Cells</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015678" MajorTopicYN="N">Viral Structural Proteins</DescriptorName><QualifierName UI="Q000032" 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Microbiol. 2020. https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15039</Citation></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li></region></list><tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Gouveia, Duarte" sort="Gouveia, Duarte" uniqKey="Gouveia D" first="Duarte" last="Gouveia">Duarte Gouveia</name></region><name sortKey="Armengaud, Jean" sort="Armengaud, Jean" uniqKey="Armengaud J" first="Jean" last="Armengaud">Jean Armengaud</name><name sortKey="Bellanger, Laurent" sort="Bellanger, Laurent" uniqKey="Bellanger L" first="Laurent" last="Bellanger">Laurent Bellanger</name><name sortKey="Gaillard, Jean Charles" sort="Gaillard, Jean Charles" uniqKey="Gaillard J" first="Jean-Charles" last="Gaillard">Jean-Charles Gaillard</name><name sortKey="Gallais, Fabrice" sort="Gallais, Fabrice" uniqKey="Gallais F" first="Fabrice" last="Gallais">Fabrice Gallais</name><name sortKey="Grenga, Lucia" sort="Grenga, Lucia" uniqKey="Grenga L" first="Lucia" last="Grenga">Lucia Grenga</name><name sortKey="Pible, Olivier" sort="Pible, Olivier" uniqKey="Pible O" first="Olivier" last="Pible">Olivier Pible</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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