Chromatographic retention time prediction for posttranslationally modified peptides

Proteomics
Luminita MoruzLukas Käll

Abstract

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 oth...Continue Reading

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Citations

Feb 20, 2014·Journal of the American Society for Mass Spectrometry·Benlian WangMark R Chance
Oct 6, 2015·Journal of Proteomics·Elisabetta GianazzaIvano Eberini
Jan 19, 2016·Journal of Proteome Research·Stephen W HolmanClaire E Eyers
Jan 23, 2016·Mass Spectrometry Reviews·Luminita Moruz, Lukas Käll
Dec 11, 2013·Proteomics·Pieter KelchtermansLennart Martens
Jul 16, 2016·The Analyst·Irina A TarasovaMikhail V Gorshkov
Feb 20, 2015·Molecular & Cellular Proteomics : MCP·Silke JacquesKris Gevaert
Mar 19, 2013·Current Protocols in Bioinformatics·Can BruceKenneth Williams
Oct 27, 2018·Analytical and Bioanalytical Chemistry·Cathrin VeenaasPeter Haglund
May 28, 2019·Nature Methods·Siegfried GessulatMathias Wilhelm
Jan 26, 2020·Proteomics·Bart Van PuyveldeMaarten Dhaenens
Apr 9, 2020·Proteomics·Robbin BouwmeesterSven Degroeve
Aug 30, 2020·Analytical and Bioanalytical Chemistry·Sergey OsipenkoYury Kostyukevich
Apr 1, 2016·Expert Review of Proteomics·Evelyne MaesDirk Valkenborg
Feb 2, 2021·Journal of Proteome Research·Carina VillacrésOleg V Krokhin
Sep 18, 2020·Proteomics·Bo WenBing Zhang
Sep 15, 2017·Journal of Proteome Research·Mark V IvanovMikhail V Gorshkov

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