Structural analysis has become a common place for understanding various molecular interactions such as epitope mapping and binding pocket identification. Here we will highlight the tools available to enhance common MS structural applications with PDB overlays to correlate mass spectrometry data with other structural techniques such as X-ray crystallography and cryo-EM. Allowing users to provide valuable visuals to understand these complex interactions and easily relay them via the reporting functions to other stakeholders.
Importing PDB files
PDB files can be imported both before and after project creation. Using the workflow a PDB file can easily be specified to bring in at creation:
Post project creation files can be brought in through the edit menu:
Regardless of which method is used the PDB files will become available in the reports to highlight key areas of interest from structural analyses from HDX, Oxidative Footprinting, etc
Interacting with PDB files
Above we can see the overlay of decreased %Deuteration illustrating the supported epitope site. This is done by selecting the correct PDB file and configuring the pivot table to display the desired data in the same way as any other heatmap in the report.
Often times the constructs used for creating the PDB file and those using in the MS analysis may differ to facilitate one of the data collection methods. Using the current tab settings option, we can adjust position offsets to align the PDB file with the fasta used in the MS analysis:
In this same menu we can adjust the colors used and set the color gradient of the heat map, allowing for a full range of customization to suit each analysis.