Mass Spectrometry &
Molecular Dynamics Simulation

1. In one recently completed project, I replicated the mass spectrometry gas phase scenarios through mobile proton molecular dynamics simulation (Trajectory Stitching approach) and umbrella sampling in GROMACS. A substantial unfolding of the studied proteins was observed in extended temperatures and higher charge states. It was a very challenging project and I had to troubleshoot for nearly 6-7 months to establish the methodology.

 A pseudo-representation is included below.

2. Previously, I also simulated (static proton MD Simulation) the ubiquitin protein across various charge states to depict the conformers associated with the most intense peaks observed in mass spectra. A gradual unfolding was observed and A-State conformer was found in 13+ charge state.

3. Currently,  I am troubleshooting on  replicating mass spectrometry ESI-ionizaion process through molecular dynamics simulation. I am working to automate the whole process.

From this training I have learned fundamentals of mass spectrometry, tandem MS/MS, assigning b & y ions, fragmentation pattern for ubiquitin by IRMPD, UVPD,  and  mass spectrum analysis

Ubiquitin Charge and Mass calculation from mass spectrum              Nomenclature of fragment ions produced on breaking C‒C,                                                                                                                       C‒N and N−C bonds in peptides and proteins 

MS/MS Spectrum for ESI-LTQ Mass Spectrometer