New mass spectrometer reveals human proteins in greater detail

A box just four-feet square is the latest addition to the analytical armory of the National Bio-Organic Biomedical Mass Spectrometry Resource Center, which is directed by Al Burlingame, PhD, a faculty member in the Department of Pharmaceutical Chemistry at the UCSF School of Pharmacy.

The diminutive US$1 million mass spectrometer is a big-time key to measuring the constant cascade of chemical changes under way in the tens of thousands of proteins that make up humans — changes that affect health, illness, and the design of pharmaceutical interventions to prevent or cure disease. Historically, it was assumed that the proteins within our cells remained relatively static after they were formed by being translated from our genetic blueprints. Now we know they are in a state of constant structural change.

The mass spectrometer, which is a Thermo-Fisher LTQ Orbitrap Velos model, was acquired with grants from the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH). It represents the latest leap forward in monitoring and measuring the molecular kaleidoscope of the human proteome.

“The technological pace in this field has been astounding — almost a revolution every 2 to 3 years, ” says Burlingame.

The latest of the resource center ’s dozen-plus instruments is no exception to that revolutionary rule. For the first time, “you can optimize sensitivity, mass resolution, and accuracy of mass measurement simultaneously, ” notes Burlingame.

Mass spectrometry vaporizes and ionizes (i.e. adds charges to) molecules, ultimately breaking them apart to sort, tote up, and identify their chemical compositions based on their mass and charge.

The new equipment combines the ability to handle relatively large biomolecules, such as human proteins, with precise techniques for dissecting them. It represents the latest version of so-called electron-transfer dissociation machines that break chemical bonds with minute, super-quick bursts of energy released by electrons drawn by electrostatic attraction to the ionized proteins.


Al Burlingame, PhD, director, National Bio-Organic Biomedical Mass Spectrometry Resource Center (left) and Jonathan Trinidad, PhD, adjunct faculty member, Department of Pharmaceutical Chemistry (right).

The technique “enables us to very surgically snap each basic bond residue, ” says Burlingame. Thus key chemical sequence and modification information is not lost in breaking up large proteins for analysis.

This allows researchers to identify “changes that are only a small percentage of the total protein, ” says Burlingame. “This instrument allows you to see these key regulatory signatures (post-translationally modified components) at lower levels. ”

Indeed, while mass spectrometry is already renowned for detecting proteins in minute sample quantities, the new instrument ’s sensitivity is 3 times greater than its 3-year-old predecessor: “A factor of 3 is a lot at this level, ” says Burlingame.

As part of a national resource center the new machine will assist biomedical researchers to examine processes such as phosphorylation, which is the addition of a phosphate group to a protein. Phosphorylation plays a key role in many cell functions, including cell division, which makes it the target of anti-cancer drugs.

Like many a cellular protein, the new mass spectrometer is only effective in the right context. In this case, it means in a facility with a staff of veteran researchers. As Burlingame, who founded the center almost 40 year ago, notes,: “How you translate the instrument ’s fundamental capability into doing research is really a matter of expertise and experience coupled with intimate continual interaction with biomedical investigators who are trying to solve cutting edge research challenges. ”

As a national resource center, the National Bio-Organic Biomedical Mass Spectrometry Resource Center collaborates with researchers throughout UCSF and beyond. Some of the UCSF researchers who will make specific use of the new mass spectrometer and who played key roles in garnering the HHMI funds for the purchase are Kevan Shokat, PhD, chair of the UCSF School of Medicine ’s Department of Cellular and Molecular Pharmacology, and Shokat ’s department colleagues Jack Taunton, PhD, and Wendell Lim, PhD; and Yuh-Nung Jan, PhD, in the UCSF School of Medicine ’s Department of Physiology.


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