Skip to main content
ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Publications at this Location » Publication #403721
Research Project: Elucidating the Factors that Determine the Ecology of Human Pathogens in Foods

Location: Produce Safety and Microbiology Research

Title: Understanding gas phase dissociation of singly charged metastable protein ions generated by MALDI using protein structures predicted by Alphafold2

Author
item PARK, JIHYUN - Orise Fellow
item Fagerquist, Clifton - Keith

Submitted to: American Chemical Society
Publication Type: Abstract Only
Publication Acceptance Date: 5/17/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying proteins from unfractionated mixtures. MS/MS allows isolation of specific protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of MS/MS post-source decay (PSD) varies widely and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have a wider access to protein structures for which no crystal structure exists. In this work, we use protein bioinformatics to explore the structural properties of bacterial proteins that can affect their gas phase dissociation. We extract the protein structural properties from Alphafold2 predictions at the residue and protein-scale level and analyze their correlation to the fragmentation efficiency of protein ions by MS/MS-PSD.