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Chromatographic retention time prediction for posttranslationally modified peptides
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2012 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 12, no 8, 1151-1159 p.Article in journal (Refereed) Published
Abstract [en]

Retention time prediction of peptides in liquid chromatography has proven to be a valuable tool for mass spectrometry-based proteomics, especially in designing more efficient procedures for state-of-the-art targeted workflows. Additionally, accurate retention time predictions can also be used to increase confidence in identifications in shotgun experiments. Despite these obvious benefits, the use of such methods has so far not been extended to (posttranslationally) modified peptides due to the absence of efficient predictors for such peptides. We here therefore describe a new retention time predictor for modified peptides, built on the foundations of our existing Elude algorithm. We evaluated our software by applying it on five types of commonly encountered modifications. Our results show that Elude now yields equally good prediction performances for modified and unmodified peptides, with correlation coefficients between predicted and observed retention times ranging from 0.93 to 0.98 for all the investigated datasets. Furthermore, we show that our predictor handles peptides carrying multiple modifications as well. This latest version of Elude is fully portable to new chromatographic conditions and can readily be applied to other types of posttranslational modifications. Elude is available under the permissive Apache2 open source License at or can be run via a web-interface at.

Place, publisher, year, edition, pages
2012. Vol. 12, no 8, 1151-1159 p.
Keyword [en]
Bioinformatics, Machine learning, Posttranslational modification, Retention time prediction, Reversed-phase liquid chromatography
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:kth:diva-96738DOI: 10.1002/pmic.201100386ISI: 000303918200009ScopusID: 2-s2.0-84860866233OAI: diva2:532967
Swedish Research CouncilEU, European Research Council, 262067-PRIME-XSSwedish e‐Science Research CenterScience for Life Laboratory - a national resource center for high-throughput molecular bioscience

QC 20120612

Available from: 2012-06-12 Created: 2012-06-11 Last updated: 2013-04-15Bibliographically approved

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Käll, Lukas
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Gene TechnologyScience for Life Laboratory, SciLifeLab
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