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Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues
[Image: see text] Hydrophilic 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 eluti...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical
Society
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937359/ https://www.ncbi.nlm.nih.gov/pubmed/29528219 http://dx.doi.org/10.1021/acs.analchem.7b05157 |
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author | Giese, Sven H. Ishihama, Yasushi Rappsilber, Juri |
author_facet | Giese, Sven H. Ishihama, Yasushi Rappsilber, Juri |
author_sort | Giese, Sven H. |
collection | PubMed |
description | [Image: see text] Hydrophilic 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. |
format | Online Article Text |
id | pubmed-5937359 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | American
Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-59373592018-05-08 Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues Giese, Sven H. Ishihama, Yasushi Rappsilber, Juri Anal Chem [Image: see text] Hydrophilic 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. American Chemical Society 2018-03-12 2018-04-03 /pmc/articles/PMC5937359/ /pubmed/29528219 http://dx.doi.org/10.1021/acs.analchem.7b05157 Text en Copyright © 2018 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Giese, Sven H. Ishihama, Yasushi Rappsilber, Juri Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues |
title | Peptide Retention in Hydrophilic Strong Anion Exchange
Chromatography Is Driven by Charged and Aromatic Residues |
title_full | Peptide Retention in Hydrophilic Strong Anion Exchange
Chromatography Is Driven by Charged and Aromatic Residues |
title_fullStr | Peptide Retention in Hydrophilic Strong Anion Exchange
Chromatography Is Driven by Charged and Aromatic Residues |
title_full_unstemmed | Peptide Retention in Hydrophilic Strong Anion Exchange
Chromatography Is Driven by Charged and Aromatic Residues |
title_short | Peptide Retention in Hydrophilic Strong Anion Exchange
Chromatography Is Driven by Charged and Aromatic Residues |
title_sort | peptide retention in hydrophilic strong anion exchange
chromatography is driven by charged and aromatic residues |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937359/ https://www.ncbi.nlm.nih.gov/pubmed/29528219 http://dx.doi.org/10.1021/acs.analchem.7b05157 |
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