Evan Hubbard   Evan Hubbard currently works as a graduate student in the Julian Lab at UC Riverside, using DIA data and gas-phase radical chemistry to find new ways of detecting amino acid isomers.

Finding and Quantifying Amino Acid Isomers in Data-independent Acquisition Data to Achieve Isomer Proteomics

Some amino acids are capable of undergoing spontaneous chemical modifications to become a structural or enantiomeric isomer of the canonical residue. Confined to an individual amino acid and massless, these modifications are notoriously difficult to detect despite potentially affecting protein structure or inhibiting enzymatic digestion. Recently, we have shown that data-independent acquisition (DIA) is capable of detecting these modifications through retention time shifts of peptides containing these isomers. Such shifts produce multiple peaks in the chromatogram of a single peptide. Read More
In DIA data from AD and control brains, a semi-automated isomer search was able to find instances of chromatograms containing multiple peptide peaks. This facilitated whole-proteome isomer detection. For discovered isomers, quantification occurred through a process of manual adjustment of integration windows for individual isomer peaks. Using this method, aspartic acid isomerization within the tau peptide TDHGAEIVYK was found to be substantially increased in diseased brains. This pathological isomerization, along with proteomic analysis of autophagy markers, has significant implications for an autophagic flux theory of Alzheimer’s disease.