Prediction of peptide ion collision cross sections from topological molecular structure and amino acid parameters

Analytical Chemistry
Philip D MosierD E Clemmer

Abstract

Quantitative structure-property relationships (QSPRs) have been developed to predict the ion mobility spectrometry (IMS) collision cross sections of singly protonated lysine-terminated peptides using information derived from topological molecular structure and various amino acid parameters. The primary amino acid sequence alone is sufficient to accurately predict the collision cross section. The models were built using multiple linear regression (MLR) and computational neural networks (CNNs). The best MLR model found contains six descriptors and predicts 94 of 113 peptides (83%) to within 2% of their experimentally determined values. The best CNN model using the same six descriptors predicts 105 of the 113 peptides (93%) to within 2% of their experimentally determined values. The best overall CNN model, using a different set of six descriptors, predicts 109 of the 113 peptides (96%) to within 2% of their experimentally determined values. In addition, this model can discriminate among peptides having identical amino acid composition, but differing in primary amino acid sequence. This represents a capability not found in previously described models. The descriptors used in the models presented may provide some insight into the na...Continue Reading

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Citations

Jun 8, 2007·Journal of the American Society for Mass Spectrometry·Xiaoyun LiuDavid E Clemmer
Nov 30, 2002·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Brandon T RuotoloDavid H Russell
Jun 24, 2017·Chemical Communications : Chem Comm·M T Soper-HopperF M Fernández
Oct 7, 2016·The Analyst·William F SiemsHerbert H Hill
May 9, 2009·European Journal of Mass Spectrometry·David P SmithAlison E Ashcroft
Jul 11, 2018·Rapid Communications in Mass Spectrometry : RCM·Sébastien HupinCarlos Afonso
Apr 27, 2010·Chemical Society Reviews·Charlotte UetrechtAlbert J R Heck
Apr 30, 2010·Analytical Chemistry·Grady Hanrahan
Jul 21, 2006·The Journal of Physical Chemistry. B·Amy E Hilderbrand, David E Clemmer
Feb 24, 2019·Journal of the American Society for Mass Spectrometry·Aarti BashyalJennifer S Brodbelt
May 10, 2017·Journal of the American Society for Mass Spectrometry·Paul W A DevineAlison E Ashcroft
Aug 9, 2005·Journal of Proteome Research·John A TaraszkaDavid E Clemmer
Jun 1, 2005·Journal of Chemical Information and Modeling·Rajarshi Guha, Peter C Jurs

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