Hydrophilic properties as a new contribution for computer-aided identification of short peptides in complex mixtures.
Identifieur interne : 000072 ( PubMed/Checkpoint ); précédent : 000071; suivant : 000073Hydrophilic properties as a new contribution for computer-aided identification of short peptides in complex mixtures.
Auteurs : Christelle Harscoat-Schiavo [France] ; Claudia Nioi ; Evelyne Ronat-Heit ; Cédric Paris ; Régis Vanderesse ; Frantz Fournier ; Ivan MarcSource :
- Analytical and bioanalytical chemistry [ 1618-2650 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Peptides.
- chemical : Complex Mixtures.
- Chromatography, Liquid, Mass Spectrometry.
Abstract
A new method to predict elementary amino acid (AA) composition of peptides (molar mass <1,000 g/mol) is described. This procedure is based on a computer-aided method using three combined analyses-reversed phase liquid chromatography (RPLC), hydrophilic interaction chromatography (HILIC) and capillary electrophoresis coupled with mass spectrometry-and using a software calculating all possible amino acid combinations from the mass of any given peptide. The complementarity between HILIC and RPLC was demonstrated. Peptide retention prediction in HILIC was successfully modelled, and the achieved prediction accuracy was as high as r²=0.97. This mathematical model, based on amino acid retention contributions and peptide length, provided the information about peptide hydrophilicity that was not redundant with its hydrophobicity. Correlations between respectively the hydrophobicity coefficients and RPLC retention time, hydrophilicity and HILIC retention time, and electrophoretic mobility and migration time were used for ranking all potential AA combinations corresponding to the given mass. The essential contribution of HILIC in this identification strategy and the need to combine the three models to significantly increase identification capabilities were both shown. Applied to an 18-standard peptide mixture, the identification procedure enabled the actual AA combination determination of the 14 di- to pentapeptides, in addition to an over 98 % reduction of possible combination numbers for the four hexapeptides. This procedure was then applied to the identification of 24 unknown peptides in a rapeseed protein hydrolysate. The effective AA composition was found for ten peptides, whereas for the 14 other peptides, the number of possible combinations was reduced by over 95 % thanks to the association of the three analyses. Finally, as a result of the information provided by the analytical techniques about peptides present in the mixture, the proposed method could become a highly valuable tool to recover bioactive peptides from undefined protein hydrolysates.
DOI: 10.1007/s00216-012-5987-6
PubMed: 22543694
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Christelle.Harscoat@ensic.inpl-nancy.fr</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Réactions et Génie des Procédés-U.P.R. 3349 C.N.R.S, Université de Lorraine, Plate forme SVS, 13 rue du bois de la Champelle, 54500 Vandœuvre-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandœuvre-lès-Nancy</settlement></placeName><orgName type="university">Université de Lorraine</orgName></affiliation></author><author><name sortKey="Nioi, Claudia" sort="Nioi, Claudia" uniqKey="Nioi C" first="Claudia" last="Nioi">Claudia Nioi</name></author><author><name sortKey="Ronat Heit, Evelyne" sort="Ronat Heit, Evelyne" uniqKey="Ronat Heit E" first="Evelyne" last="Ronat-Heit">Evelyne Ronat-Heit</name></author><author><name sortKey="Paris, Cedric" sort="Paris, Cedric" uniqKey="Paris C" first="Cédric" last="Paris">Cédric Paris</name></author><author><name sortKey="Vanderesse, Regis" sort="Vanderesse, Regis" uniqKey="Vanderesse R" first="Régis" last="Vanderesse">Régis Vanderesse</name></author><author><name sortKey="Fournier, Frantz" sort="Fournier, Frantz" uniqKey="Fournier F" first="Frantz" last="Fournier">Frantz Fournier</name></author><author><name sortKey="Marc, Ivan" sort="Marc, Ivan" uniqKey="Marc I" first="Ivan" last="Marc">Ivan Marc</name></author></analytic><series><title level="j">Analytical and bioanalytical chemistry</title><idno type="eISSN">1618-2650</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromatography, Liquid</term><term>Complex Mixtures</term><term>Mass Spectrometry</term><term>Peptides (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chromatographie en phase liquide</term><term>Mélanges complexes</term><term>Peptides ()</term><term>Spectrométrie de masse</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptides</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Complex Mixtures</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromatography, Liquid</term><term>Mass Spectrometry</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chromatographie en phase liquide</term><term>Mélanges complexes</term><term>Peptides</term><term>Spectrométrie de masse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A new method to predict elementary amino acid (AA) composition of peptides (molar mass <1,000 g/mol) is described. This procedure is based on a computer-aided method using three combined analyses-reversed phase liquid chromatography (RPLC), hydrophilic interaction chromatography (HILIC) and capillary electrophoresis coupled with mass spectrometry-and using a software calculating all possible amino acid combinations from the mass of any given peptide. The complementarity between HILIC and RPLC was demonstrated. Peptide retention prediction in HILIC was successfully modelled, and the achieved prediction accuracy was as high as r²=0.97. This mathematical model, based on amino acid retention contributions and peptide length, provided the information about peptide hydrophilicity that was not redundant with its hydrophobicity. Correlations between respectively the hydrophobicity coefficients and RPLC retention time, hydrophilicity and HILIC retention time, and electrophoretic mobility and migration time were used for ranking all potential AA combinations corresponding to the given mass. The essential contribution of HILIC in this identification strategy and the need to combine the three models to significantly increase identification capabilities were both shown. Applied to an 18-standard peptide mixture, the identification procedure enabled the actual AA combination determination of the 14 di- to pentapeptides, in addition to an over 98 % reduction of possible combination numbers for the four hexapeptides. This procedure was then applied to the identification of 24 unknown peptides in a rapeseed protein hydrolysate. The effective AA composition was found for ten peptides, whereas for the 14 other peptides, the number of possible combinations was reduced by over 95 % thanks to the association of the three analyses. Finally, as a result of the information provided by the analytical techniques about peptides present in the mixture, the proposed method could become a highly valuable tool to recover bioactive peptides from undefined protein hydrolysates.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">22543694</PMID><DateCreated><Year>2012</Year><Month>05</Month><Day>23</Day></DateCreated><DateCompleted><Year>2012</Year><Month>09</Month><Day>17</Day></DateCompleted><DateRevised><Year>2016</Year><Month>05</Month><Day>12</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1618-2650</ISSN><JournalIssue CitedMedium="Internet"><Volume>403</Volume><Issue>7</Issue><PubDate><Year>2012</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Analytical and bioanalytical chemistry</Title><ISOAbbreviation>Anal Bioanal Chem</ISOAbbreviation></Journal><ArticleTitle>Hydrophilic properties as a new contribution for computer-aided identification of short peptides in complex mixtures.</ArticleTitle><Pagination><MedlinePgn>1939-49</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00216-012-5987-6</ELocationID><Abstract><AbstractText>A new method to predict elementary amino acid (AA) composition of peptides (molar mass <1,000 g/mol) is described. This procedure is based on a computer-aided method using three combined analyses-reversed phase liquid chromatography (RPLC), hydrophilic interaction chromatography (HILIC) and capillary electrophoresis coupled with mass spectrometry-and using a software calculating all possible amino acid combinations from the mass of any given peptide. The complementarity between HILIC and RPLC was demonstrated. Peptide retention prediction in HILIC was successfully modelled, and the achieved prediction accuracy was as high as r²=0.97. This mathematical model, based on amino acid retention contributions and peptide length, provided the information about peptide hydrophilicity that was not redundant with its hydrophobicity. Correlations between respectively the hydrophobicity coefficients and RPLC retention time, hydrophilicity and HILIC retention time, and electrophoretic mobility and migration time were used for ranking all potential AA combinations corresponding to the given mass. The essential contribution of HILIC in this identification strategy and the need to combine the three models to significantly increase identification capabilities were both shown. Applied to an 18-standard peptide mixture, the identification procedure enabled the actual AA combination determination of the 14 di- to pentapeptides, in addition to an over 98 % reduction of possible combination numbers for the four hexapeptides. This procedure was then applied to the identification of 24 unknown peptides in a rapeseed protein hydrolysate. The effective AA composition was found for ten peptides, whereas for the 14 other peptides, the number of possible combinations was reduced by over 95 % thanks to the association of the three analyses. Finally, as a result of the information provided by the analytical techniques about peptides present in the mixture, the proposed method could become a highly valuable tool to recover bioactive peptides from undefined protein hydrolysates.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Harscoat-Schiavo</LastName><ForeName>Christelle</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Laboratoire Réactions et Génie des Procédés-U.P.R. 3349 C.N.R.S, Université de Lorraine, Plate forme SVS, 13 rue du bois de la Champelle, 54500 Vandœuvre-lès-Nancy, France. Christelle.Harscoat@ensic.inpl-nancy.fr</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nioi</LastName><ForeName>Claudia</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Ronat-Heit</LastName><ForeName>Evelyne</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Paris</LastName><ForeName>Cédric</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Vanderesse</LastName><ForeName>Régis</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Fournier</LastName><ForeName>Frantz</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Marc</LastName><ForeName>Ivan</ForeName><Initials>I</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D023361">Validation Studies</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>04</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Anal Bioanal Chem</MedlineTA><NlmUniqueID>101134327</NlmUniqueID><ISSNLinking>1618-2642</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D045424">Complex Mixtures</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010455">Peptides</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D002853">Chromatography, Liquid</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D045424">Complex Mixtures</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D013058">Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D010455">Peptides</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000737">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>2</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>3</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>3</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="aheadofprint"><Year>2012</Year><Month>4</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>5</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>5</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>9</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="doi">10.1007/s00216-012-5987-6</ArticleId><ArticleId IdType="pubmed">22543694</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Vandœuvre-lès-Nancy</li></settlement><orgName><li>Université de Lorraine</li></orgName></list><tree><noCountry><name sortKey="Fournier, Frantz" sort="Fournier, Frantz" uniqKey="Fournier F" first="Frantz" last="Fournier">Frantz Fournier</name><name sortKey="Marc, Ivan" sort="Marc, Ivan" uniqKey="Marc I" first="Ivan" last="Marc">Ivan Marc</name><name sortKey="Nioi, Claudia" sort="Nioi, Claudia" uniqKey="Nioi C" first="Claudia" last="Nioi">Claudia Nioi</name><name sortKey="Paris, Cedric" sort="Paris, Cedric" uniqKey="Paris C" first="Cédric" last="Paris">Cédric Paris</name><name sortKey="Ronat Heit, Evelyne" sort="Ronat Heit, Evelyne" uniqKey="Ronat Heit E" first="Evelyne" last="Ronat-Heit">Evelyne Ronat-Heit</name><name sortKey="Vanderesse, Regis" sort="Vanderesse, Regis" uniqKey="Vanderesse R" first="Régis" last="Vanderesse">Régis Vanderesse</name></noCountry><country name="France"><region name="Grand Est"><name sortKey="Harscoat Schiavo, Christelle" sort="Harscoat Schiavo, Christelle" uniqKey="Harscoat Schiavo C" first="Christelle" last="Harscoat-Schiavo">Christelle Harscoat-Schiavo</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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