Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies
SARS‐CoV‐2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS‐CoV‐2, identifying potential T cell epitopes derived from the SARS‐CoV‐2 proteome. Such studies will aid in identifying targets for vaccination and immu...
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| Veröffentlicht in: | Proteomics (Weinheim) 2021-09, Vol.21 (17-18), p.e2100036-n/a |
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| creator | Li, Chen Revote, Jerico Ramarathinam, Sri H. Chung, Shan Zou Croft, Nathan P. Scull, Katherine E. Huang, Ziyi Ayala, Rochelle Braun, Asolina Mifsud, Nicole A. Illing, Patricia T. Faridi, Pouya Purcell, Anthony W. |
| description | SARS‐CoV‐2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS‐CoV‐2, identifying potential T cell epitopes derived from the SARS‐CoV‐2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS‐CoV‐2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user‐friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide‐HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS. |
| doi_str_mv | 10.1002/pmic.202100036 |
| format | Article |
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A number of studies have examined the T cell mediated immune responses against SARS‐CoV‐2, identifying potential T cell epitopes derived from the SARS‐CoV‐2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS‐CoV‐2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user‐friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide‐HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.</description><identifier>ISSN: 1615-9853</identifier><identifier>EISSN: 1615-9861</identifier><identifier>DOI: 10.1002/pmic.202100036</identifier><identifier>PMID: 33811468</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Annotations ; Antigens ; Browsing ; COVID-19 ; COVID19 ; Epitopes ; Histocompatibility antigen HLA ; Humans ; Immunology ; Knowledge bases (artificial intelligence) ; LC–MS ; Leukocytes ; Lymphocytes ; Lymphocytes T ; Mass spectrometry ; Mass spectroscopy ; Pandemics ; Peptides ; Proteomes ; Proteomics ; SARS-CoV-2 ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Spectra ; Synthetic peptides ; Tandem Mass Spectrometry ; Vaccination</subject><ispartof>Proteomics (Weinheim), 2021-09, Vol.21 (17-18), p.e2100036-n/a</ispartof><rights>2021 Wiley‐VCH GmbH</rights><rights>2021 Wiley-VCH GmbH.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4921-a034600b96efbb14f895b2ccd069db962faf635906f4600e39f4b0b64de02c0d3</citedby><cites>FETCH-LOGICAL-c4921-a034600b96efbb14f895b2ccd069db962faf635906f4600e39f4b0b64de02c0d3</cites><orcidid>0000-0002-2128-5127 ; 0000-0002-2712-3356 ; 0000-0003-0532-8331 ; 0000-0002-2787-1282 ; 0000-0002-1847-754X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fpmic.202100036$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fpmic.202100036$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33811468$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Chen</creatorcontrib><creatorcontrib>Revote, Jerico</creatorcontrib><creatorcontrib>Ramarathinam, Sri H.</creatorcontrib><creatorcontrib>Chung, Shan Zou</creatorcontrib><creatorcontrib>Croft, Nathan P.</creatorcontrib><creatorcontrib>Scull, Katherine E.</creatorcontrib><creatorcontrib>Huang, Ziyi</creatorcontrib><creatorcontrib>Ayala, Rochelle</creatorcontrib><creatorcontrib>Braun, Asolina</creatorcontrib><creatorcontrib>Mifsud, Nicole A.</creatorcontrib><creatorcontrib>Illing, Patricia T.</creatorcontrib><creatorcontrib>Faridi, Pouya</creatorcontrib><creatorcontrib>Purcell, Anthony W.</creatorcontrib><title>Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies</title><title>Proteomics (Weinheim)</title><addtitle>Proteomics</addtitle><description>SARS‐CoV‐2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS‐CoV‐2, identifying potential T cell epitopes derived from the SARS‐CoV‐2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS‐CoV‐2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user‐friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide‐HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.</description><subject>Annotations</subject><subject>Antigens</subject><subject>Browsing</subject><subject>COVID-19</subject><subject>COVID19</subject><subject>Epitopes</subject><subject>Histocompatibility antigen HLA</subject><subject>Humans</subject><subject>Immunology</subject><subject>Knowledge bases (artificial intelligence)</subject><subject>LC–MS</subject><subject>Leukocytes</subject><subject>Lymphocytes</subject><subject>Lymphocytes T</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Pandemics</subject><subject>Peptides</subject><subject>Proteomes</subject><subject>Proteomics</subject><subject>SARS-CoV-2</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Spectra</subject><subject>Synthetic peptides</subject><subject>Tandem Mass Spectrometry</subject><subject>Vaccination</subject><issn>1615-9853</issn><issn>1615-9861</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9u3CAQxlHUKv-vOVaWesmhuxnAxuZSKVq16UqpGu22uSKMYUNkG8fYqfa2j5BnzJOUrTdW2ksOwAz85tMwH0JnGKYYgFw0lVVTAiQkQNkeOsQMJxOeMfxujBN6gI68vwfAacbTfXRAaYZxzLJDtFlo7_pW2Xr1KZJ17TrZ7eIiLFmufUgjv667O91ZFTW66WyhfeRMtLxcLJ83TzN3G3YSGddGtqr62g2QC735v0IuFL-8lW5llSwj3_WF1f4EvTey9Pp0dx6jX1-__Jx9m1z_uJrPLq8nKuYETyTQmAHknGmT5zg2GU9yolQBjBfhlhhpGE04MLPlNOUmziFncaGBKCjoMfo86DZ9XulC6bprZSma1layXQsnrfj3pbZ3YuUeRUYSIGkWBM53Aq176LXvRGW90mUpa-16LwKWJSnjhAb043_ofZhxGOaWSoMrPMU4UNOBUq3zvtVmbAaD2JortuaK0dxQ8OH1F0b8xc0AJAPw25Z6_YacuPk-n2EaA6Z_AKKHtP4</recordid><startdate>202109</startdate><enddate>202109</enddate><creator>Li, Chen</creator><creator>Revote, Jerico</creator><creator>Ramarathinam, Sri H.</creator><creator>Chung, Shan Zou</creator><creator>Croft, Nathan P.</creator><creator>Scull, Katherine E.</creator><creator>Huang, Ziyi</creator><creator>Ayala, Rochelle</creator><creator>Braun, Asolina</creator><creator>Mifsud, Nicole A.</creator><creator>Illing, Patricia T.</creator><creator>Faridi, Pouya</creator><creator>Purcell, Anthony W.</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-2128-5127</orcidid><orcidid>https://orcid.org/0000-0002-2712-3356</orcidid><orcidid>https://orcid.org/0000-0003-0532-8331</orcidid><orcidid>https://orcid.org/0000-0002-2787-1282</orcidid><orcidid>https://orcid.org/0000-0002-1847-754X</orcidid></search><sort><creationdate>202109</creationdate><title>Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies</title><author>Li, Chen ; Revote, Jerico ; Ramarathinam, Sri H. ; Chung, Shan Zou ; Croft, Nathan P. ; Scull, Katherine E. ; Huang, Ziyi ; Ayala, Rochelle ; Braun, Asolina ; Mifsud, Nicole A. ; Illing, Patricia T. ; Faridi, Pouya ; Purcell, Anthony W.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4921-a034600b96efbb14f895b2ccd069db962faf635906f4600e39f4b0b64de02c0d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Annotations</topic><topic>Antigens</topic><topic>Browsing</topic><topic>COVID-19</topic><topic>COVID19</topic><topic>Epitopes</topic><topic>Histocompatibility antigen HLA</topic><topic>Humans</topic><topic>Immunology</topic><topic>Knowledge bases (artificial intelligence)</topic><topic>LC–MS</topic><topic>Leukocytes</topic><topic>Lymphocytes</topic><topic>Lymphocytes T</topic><topic>Mass spectrometry</topic><topic>Mass spectroscopy</topic><topic>Pandemics</topic><topic>Peptides</topic><topic>Proteomes</topic><topic>Proteomics</topic><topic>SARS-CoV-2</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Spectra</topic><topic>Synthetic peptides</topic><topic>Tandem Mass Spectrometry</topic><topic>Vaccination</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Chen</creatorcontrib><creatorcontrib>Revote, Jerico</creatorcontrib><creatorcontrib>Ramarathinam, Sri H.</creatorcontrib><creatorcontrib>Chung, Shan Zou</creatorcontrib><creatorcontrib>Croft, Nathan P.</creatorcontrib><creatorcontrib>Scull, Katherine E.</creatorcontrib><creatorcontrib>Huang, Ziyi</creatorcontrib><creatorcontrib>Ayala, Rochelle</creatorcontrib><creatorcontrib>Braun, Asolina</creatorcontrib><creatorcontrib>Mifsud, Nicole A.</creatorcontrib><creatorcontrib>Illing, Patricia T.</creatorcontrib><creatorcontrib>Faridi, Pouya</creatorcontrib><creatorcontrib>Purcell, Anthony W.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proteomics (Weinheim)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Chen</au><au>Revote, Jerico</au><au>Ramarathinam, Sri H.</au><au>Chung, Shan Zou</au><au>Croft, Nathan P.</au><au>Scull, Katherine E.</au><au>Huang, Ziyi</au><au>Ayala, Rochelle</au><au>Braun, Asolina</au><au>Mifsud, Nicole A.</au><au>Illing, Patricia T.</au><au>Faridi, Pouya</au><au>Purcell, Anthony W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies</atitle><jtitle>Proteomics (Weinheim)</jtitle><addtitle>Proteomics</addtitle><date>2021-09</date><risdate>2021</risdate><volume>21</volume><issue>17-18</issue><spage>e2100036</spage><epage>n/a</epage><pages>e2100036-n/a</pages><issn>1615-9853</issn><eissn>1615-9861</eissn><abstract>SARS‐CoV‐2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS‐CoV‐2, identifying potential T cell epitopes derived from the SARS‐CoV‐2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS‐CoV‐2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user‐friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide‐HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>33811468</pmid><doi>10.1002/pmic.202100036</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-2128-5127</orcidid><orcidid>https://orcid.org/0000-0002-2712-3356</orcidid><orcidid>https://orcid.org/0000-0003-0532-8331</orcidid><orcidid>https://orcid.org/0000-0002-2787-1282</orcidid><orcidid>https://orcid.org/0000-0002-1847-754X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Annotations Antigens Browsing COVID-19 COVID19 Epitopes Histocompatibility antigen HLA Humans Immunology Knowledge bases (artificial intelligence) LC–MS Leukocytes Lymphocytes Lymphocytes T Mass spectrometry Mass spectroscopy Pandemics Peptides Proteomes Proteomics SARS-CoV-2 Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Spectra Synthetic peptides Tandem Mass Spectrometry Vaccination |
| title | Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies |
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