Epitope identification from fixed-complexity random-sequence peptide microarrays.
Identifieur interne : 001561 ( PubMed/Checkpoint ); précédent : 001560; suivant : 001562Epitope identification from fixed-complexity random-sequence peptide microarrays.
Auteurs : Josh Richer [États-Unis] ; Stephen Albert Johnston [États-Unis] ; Phillip Stafford [États-Unis]Source :
- Molecular & cellular proteomics : MCP [ 1535-9484 ] ; 2015.
Descripteurs français
- KwdFr :
- Algorithmes, Analyse par réseau de protéines, Anticorps monoclonaux (), Cartographie peptidique (), Cartographie épitopique (), Coqueluche (immunologie), Dengue (immunologie), Humains, Hépatite B (immunologie), Maladie de Lyme (immunologie), Paludisme (immunologie), Peptides (), Syphilis (immunologie), Séquence d'acides aminés, Épitopes ().
- MESH :
English descriptors
- KwdEn :
- Algorithms, Amino Acid Sequence, Antibodies, Monoclonal (chemistry), Dengue (immunology), Epitope Mapping (methods), Epitopes (chemistry), Hepatitis B (immunology), Humans, Lyme Disease (immunology), Malaria (immunology), Peptide Mapping (methods), Peptides (chemistry), Protein Array Analysis, Syphilis (immunology), Whooping Cough (immunology).
- MESH :
- chemical , chemistry : Antibodies, Monoclonal, Epitopes, Peptides.
- immunology : Dengue, Hepatitis B, Lyme Disease, Malaria, Syphilis, Whooping Cough.
- methods : Epitope Mapping, Peptide Mapping.
- Algorithms, Amino Acid Sequence, Humans, Protein Array Analysis.
Abstract
Antibodies play an important role in modern science and medicine. They are essential in many biological assays and have emerged as an important class of therapeutics. Unfortunately, current methods for mapping antibody epitopes require costly synthesis or enrichment steps, and no low-cost universal platform exists. In order to address this, we tested a random-sequence peptide microarray consisting of over 330,000 unique peptide sequences sampling 83% of all possible tetramers and 27% of pentamers. It is a single, unbiased platform that can be used in many different types of tests, it does not rely on informatic selection of peptides for a particular proteome, and it does not require iterative rounds of selection. In order to optimize the platform, we developed an algorithm that considers the significance of k-length peptide subsequences (k-mers) within selected peptides that come from the microarray. We tested eight monoclonal antibodies and seven infectious disease cohorts. The method correctly identified five of the eight monoclonal epitopes and identified both reported and unreported epitope candidates in the infectious disease cohorts. This algorithm could greatly enhance the utility of random-sequence peptide microarrays by enabling rapid epitope mapping and antigen identification.
DOI: 10.1074/mcp.M114.043513
PubMed: 25368412
Affiliations:
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type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Antibodies, Monoclonal (chemistry)</term><term>Dengue (immunology)</term><term>Epitope Mapping (methods)</term><term>Epitopes (chemistry)</term><term>Hepatitis B (immunology)</term><term>Humans</term><term>Lyme Disease (immunology)</term><term>Malaria (immunology)</term><term>Peptide Mapping (methods)</term><term>Peptides (chemistry)</term><term>Protein Array Analysis</term><term>Syphilis (immunology)</term><term>Whooping Cough (immunology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse par réseau de protéines</term><term>Anticorps monoclonaux ()</term><term>Cartographie peptidique ()</term><term>Cartographie épitopique ()</term><term>Coqueluche (immunologie)</term><term>Dengue (immunologie)</term><term>Humains</term><term>Hépatite B (immunologie)</term><term>Maladie de Lyme (immunologie)</term><term>Paludisme (immunologie)</term><term>Peptides ()</term><term>Syphilis (immunologie)</term><term>Séquence d'acides aminés</term><term>Épitopes ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Antibodies, Monoclonal</term><term>Epitopes</term><term>Peptides</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Coqueluche</term><term>Dengue</term><term>Hépatite B</term><term>Maladie de Lyme</term><term>Paludisme</term><term>Syphilis</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Dengue</term><term>Hepatitis B</term><term>Lyme Disease</term><term>Malaria</term><term>Syphilis</term><term>Whooping Cough</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Epitope Mapping</term><term>Peptide Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Humans</term><term>Protein Array Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse par réseau de protéines</term><term>Anticorps monoclonaux</term><term>Cartographie peptidique</term><term>Cartographie épitopique</term><term>Humains</term><term>Peptides</term><term>Séquence d'acides aminés</term><term>Épitopes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Antibodies play an important role in modern science and medicine. They are essential in many biological assays and have emerged as an important class of therapeutics. Unfortunately, current methods for mapping antibody epitopes require costly synthesis or enrichment steps, and no low-cost universal platform exists. In order to address this, we tested a random-sequence peptide microarray consisting of over 330,000 unique peptide sequences sampling 83% of all possible tetramers and 27% of pentamers. It is a single, unbiased platform that can be used in many different types of tests, it does not rely on informatic selection of peptides for a particular proteome, and it does not require iterative rounds of selection. In order to optimize the platform, we developed an algorithm that considers the significance of k-length peptide subsequences (k-mers) within selected peptides that come from the microarray. We tested eight monoclonal antibodies and seven infectious disease cohorts. The method correctly identified five of the eight monoclonal epitopes and identified both reported and unreported epitope candidates in the infectious disease cohorts. This algorithm could greatly enhance the utility of random-sequence peptide microarrays by enabling rapid epitope mapping and antigen identification. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25368412</PMID><DateCompleted><Year>2015</Year><Month>09</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1535-9484</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>1</Issue><PubDate><Year>2015</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Molecular & cellular proteomics : MCP</Title><ISOAbbreviation>Mol. Cell Proteomics</ISOAbbreviation></Journal><ArticleTitle>Epitope identification from fixed-complexity random-sequence peptide microarrays.</ArticleTitle><Pagination><MedlinePgn>136-47</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1074/mcp.M114.043513</ELocationID><Abstract><AbstractText>Antibodies play an important role in modern science and medicine. They are essential in many biological assays and have emerged as an important class of therapeutics. Unfortunately, current methods for mapping antibody epitopes require costly synthesis or enrichment steps, and no low-cost universal platform exists. In order to address this, we tested a random-sequence peptide microarray consisting of over 330,000 unique peptide sequences sampling 83% of all possible tetramers and 27% of pentamers. It is a single, unbiased platform that can be used in many different types of tests, it does not rely on informatic selection of peptides for a particular proteome, and it does not require iterative rounds of selection. In order to optimize the platform, we developed an algorithm that considers the significance of k-length peptide subsequences (k-mers) within selected peptides that come from the microarray. We tested eight monoclonal antibodies and seven infectious disease cohorts. The method correctly identified five of the eight monoclonal epitopes and identified both reported and unreported epitope candidates in the infectious disease cohorts. This algorithm could greatly enhance the utility of random-sequence peptide microarrays by enabling rapid epitope mapping and antigen identification. </AbstractText><CopyrightInformation>© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Richer</LastName><ForeName>Josh</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>From *Arizona State University, Tempe, Arizona 85287.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Johnston</LastName><ForeName>Stephen Albert</ForeName><Initials>SA</Initials><AffiliationInfo><Affiliation>From *Arizona State University, Tempe, Arizona 85287.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stafford</LastName><ForeName>Phillip</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>From *Arizona State University, Tempe, Arizona 85287 phillip.stafford@asu.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>11</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Cell Proteomics</MedlineTA><NlmUniqueID>101125647</NlmUniqueID><ISSNLinking>1535-9476</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000911">Antibodies, Monoclonal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000939">Epitopes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010455">Peptides</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000911" MajorTopicYN="N">Antibodies, Monoclonal</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003715" MajorTopicYN="N">Dengue</DescriptorName><QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018604" MajorTopicYN="N">Epitope Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000939" MajorTopicYN="N">Epitopes</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006509" MajorTopicYN="N">Hepatitis B</DescriptorName><QualifierName UI="Q000276" 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