IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol


  • Author contributions: RVC implemented the computational methods, selected the peptides for the testing set, executed the experiments, and wrote the first draft of the manuscript. DLF measured and provided the experimental data for the training set, contributed with insights for protocol development, and helped write and revise the manuscript. KSG defined and coordinated the computational strategies for improved performance, suggested and analyzed parameters to improve accuracy, and helped write and revise the manuscript. RDL devised the molecular simulation protocol, analyzed experiments results, proposed the modified version for the Amber99 force field, and helped write and revise the manuscript. All authors read and agreed with the final version of this article.


Introduction of ion mobility mass spectrometry (IMS/MS) into the proteomic workflow provides an orthogonal separation to the widely used LC-MS platforms. IMS also provides structural information that could facilitate peptide identification. However, the lack of tools capable of predictive power in a high-throughput fashion makes peptide global profiling quite challenging. To target this issue, a computational workflow was developed based on biophysical principles to predict the collision cross-section area (CCS) of peptides as measured from IMS/MS experiments. Hosted on a web server, it allows the user to input a primary sequence (query) and retrieve information on peptide structure, sequence, and corresponding CCS. The current version is designed to identify peptide sequences up to 23 residues in length, in its higher charge state, based on a match of the molecule m/z and CCS. The protocol was validated against a 128-sequences-dataset and CCS predicted within 2.8% average error. © 2013 Wiley Periodicals, Inc.