Simulation of Ion Mobility Spectrometry Experiments

Collaborators: Cox lab (https://www.biochem.mpg.de/cox) Max Planck Institute of Biochemistry, Research Group Computational Systems Biochemistry

Simulation of a small peptide in low pressure air (2.7 mbar) and an electric field show that the peptides accelerate due to the electric field but reach a terminal velocity because of the collisions with the air. Greenish colors show center of mass velocity of individual trajectories, red line show the average drift speed, black line indicate a fitted theoretical function. Dotted red line shows expected velocity in complete vacuum. In this simulation environment the peptide reaches an expected terminal speed of 132 m/s.

© MPI-NAT Daniel Szöllösi

Simulation of a small peptide in low pressure air (2.7 mbar) and an electric field show that the peptides accelerate due to the electric field but reach a terminal velocity because of the collisions with the air. Greenish colors show center of mass velocity of individual trajectories, red line show the average drift speed, black line indicate a fitted theoretical function. Dotted red line shows expected velocity in complete vacuum. In this simulation environment the peptide reaches an expected terminal speed of 132 m/s.

© MPI-NAT Daniel Szöllösi

Mass spectrometry based proteomics is becoming an invaluable analysis tool of complex samples like human cell lysates and allows the identification and quantification of thousands of proteins. To enhance the coverage and accuracy of complete proteomes the digested proteins are initially separated with HPLC and in latest devices additionally by trapped ion mobility spectrometry (TIMS). Ion mobility spectrometry enables differentiation of peptides based on their mass, size, shape and charge distribution. However, a deeper understanding of the peptide conformation in the low pressure environment of the drift tube would help the interpretation of the measurement results and foster instrument development.

Therefore, we carried out molecular dynamics simulations of a model peptide in low pressure air (2.7 mbar). Simulation parameters were carefully adjusted to reproduce the experimental conditions as close as possible. Drift speed obtained from simulations show a decent agreement with experimental measurement e.g. 60 m/s versus 78 m/s, respectively.