Peptide retention in hydrophilic strong anion exchange chromatography is driven by charged and aromatic residues

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dc.contributor.authorGiese, Sven H.
dc.contributor.authorIshihama, Yasushi
dc.contributor.authorRappsilber, Juri
dc.date.accessioned2021-03-11T08:01:02Z
dc.date.available2021-03-11T08:01:02Z
dc.date.issued2018-03-12
dc.description.abstractHydrophilic strong anion exchange chromatography (hSAX) is becoming a popular method for the prefractionation of proteomic samples. However, the use and further development of this approach is affected by the limited understanding of its retention mechanism and the absence of elution time prediction. Using a set of 59 297 confidentially identified peptides, we performed an explorative analysis and built a predictive deep learning model. As expected, charged residues are the major contributors to the retention time through electrostatic interactions. Aspartic acid and glutamic acid have a strong retaining effect and lysine and arginine have a strong repulsion effect. In addition, we also find the involvement of aromatic amino acids. This suggests a substantial contribution of cation−π interactions to the retention mechanism. The deep learning approach was validated using 5-fold cross-validation (CV) yielding a mean prediction accuracy of 70% during CV and 68% on a hold-out validation set. The results of this study emphasize that not only electrostatic interactions but rather diverse types of interactions must be integrated to build a reliable hSAX retention time predictor.en
dc.identifier.eissn1520-6882
dc.identifier.issn0003-2700
dc.identifier.pmid29528219
dc.identifier.urihttps://depositonce.tu-berlin.de/handle/11303/12782
dc.identifier.urihttp://dx.doi.org/10.14279/depositonce-11582
dc.language.isoenen
dc.relation.ispartof10.14279/depositonce-12031en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subject.ddc570 Biowissenschaften; Biologiede
dc.subject.otherbioinformaticsen
dc.subject.otherproteomicsen
dc.subject.otherdeep learningen
dc.titlePeptide retention in hydrophilic strong anion exchange chromatography is driven by charged and aromatic residuesen
dc.typeArticleen
dc.type.versionpublishedVersionen
dcterms.bibliographicCitation.doi10.1021/acs.analchem.7b05157en
dcterms.bibliographicCitation.issue7en
dcterms.bibliographicCitation.journaltitleAnalytical Chemistryen
dcterms.bibliographicCitation.originalpublishernameAmerican Chemical Society (ACS)en
dcterms.bibliographicCitation.originalpublisherplaceColumbus, Ohioen
dcterms.bibliographicCitation.pageend4640en
dcterms.bibliographicCitation.pagestart4635en
dcterms.bibliographicCitation.volume90en
tub.accessrights.dnbfreeen
tub.affiliationFak. 3 Prozesswissenschaften::Inst. Biotechnologie::FG Bioanalytikde
tub.affiliation.facultyFak. 3 Prozesswissenschaftende
tub.affiliation.groupFG Bioanalytikde
tub.affiliation.instituteInst. Biotechnologiede
tub.publisher.universityorinstitutionTechnische Universität Berlinen

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