Q: Why would it make a difference how mass is measured?
A: If the phrases ‘regulated enzymatic transduction’ and ‘mass spectrometry’ (MS) don’t light up similar networks in your corpus callosum, you may be laboring under the conventional wisdom imparted from your last brush with organic chemistry. The state of the art has changed dramatically and there’s never been a better time to catch up on biological MS applications now that we have remodeled and retooled the Core in 355 EMRB to support metabolomics and proteomics tooled with the most recent generation of instruments designed to do the job. Let’s explain how that makes it cheaper and quicker to reach definitive answers and better-framed quantitative questions for Systems Biology.
All MS instruments are already programmable and designed to intelligently control the high performance chromatography systems that feed them. This means the data acquisition device can, on-the-fly, devise a novel scheme consisting of isolation, purposeful activation and full scan detection with parts per million accuracy given any of a thousand circumstances that crop up during an experiment. Even with a sequential stream of rare events these instruments execute procedural changes to compensate and no sample is wasted. Cool, right! These new "orbitrap" instruments can do far more. They are synchronously multifunctional, designed to measure mass by frequency instead of flight time, and they can use electrodynamic traps to accumulate ions and select a strategy to disassemble ions based on any unique structural elements found.
So, for example, the presence of a phosphate endows a peptide with distinct mass shift and its daughter ions with easily recognized higher order response in decomposition events. These characteristics can be used to selectively record such PTM while skipping through their unmodified cousins. Further, ubiquitin modifications confer an extended sequence gap that identifies target lysine isopeptide residue. Moreover, glycopeptides can be distinguished by a bar-code of low mass oxonium chains. Lipid adducts also have signature patterns.
These new instruments are ideally suited to ferret PTM structures from complex mixtures and can do so quantitatively because a) they are hybrid instruments in one package and b) they convert mass into frequency instead of flight time. Frequency can be measured far more accurately.
Visit or contact the core facilities in room 355 EMRB and ask about the incredible level of detail that is now at your fingertips. Also, please stay tuned for future blog posts that will highlight short case studies on the questions and solutions that flow from these collaborative efforts at the University of Iowa CCOM.
Date:
Monday, December 13, 2021