Pharm Chem 219:Mass Spectrometry-based Proteomics

Spring 2022

Mass spectrometry is comprised of a broad suite of advanced technologies possessing operator adjustable suites of computer-controlled functions that allow the versatile manipulation and recording of charged molecules. These functions can be employed for the detection and identification of unknown structures in most classes of biomolecules (and a large number of other molecules and elements as well). Proteomics is broadly concerned with the gaining new knowledge on global protein composition of cells, sub-cellular organelles, complexes and machines and how their functions are modulated by posttranslational dynamics, e.g. kinome or ubiquitylome/proteasome homeostasis and dynamics and the effects of molecular defects on aberrant signaling pathways and networks, etc.

Currently major efforts are being devoted to the discovery of new members of protein complexes or complex mixtures of proteins per se. Many of these are being revealed by proximity biotinylation (bioID, APEX, BAR). In addition, considerable effort is being focused on the detection and assignment of protein covalent modifications; to the analyses of modification-site-specific protein network signaling kinetics/dynamics; and to studies of intact protein complexes, e.g. pol II, nucleosomes, etc.

Mini Course Description: This course will focus on the practical aspects (i.e. experimental and mass spectral interpretation) involved in the identification of proteins and their covalent modifications. It will cover the fundamental principles of currently important mass spectrometry instrument platforms. It will provide an overview of key scientific problems that are being tackled and solved at the protein level relevant to cell function/dysfunction; the detection and assignment of protein posttranslational modifications; and studies of site-specific dynamics/relative quantitation. It will also cover studies on the architecture of protein complexes and machines.

Methods for sample preparation and mass spectral data acquisition will be discussed together with how our UCSF bioinformatics toolbox (ProteinProspector) may be employed to facilitate the interpretation and presentation of mass spectral information.

Simultaneously, dry laboratory work is required to learn how to carry out the interpretation of complex mixtures of peptides isolated from cells involved in current active research projects. Initially blocks of time will be scheduled for class discussion of the experimental results you obtain.

Lecture Schedule: April 18 – May 6, 2022;
Tu 1.00-3.00p and Th 1-3pm

Mission Bay Campus,
Labs by arrangement; Quizzes and talks will be scheduled.

Lecture Lecturer Topic
1(T 19th) RJC Protein Identification. Basics of peptide fragmentation processes. Database searching. How to measure the reliability of assignments.
2(Th 21st) ALB Fundamentals: Ionization, Instrumentation; ion optics, resolution and mass accuracy; why these are important at protein vs peptide level.
3(Tu 26th) JO Sample preparation: Gels and Chromatography; IP/Affinity Tags, Digestion. What shouldn't be in the sample - Contaminants.
4(Th 28th) AU Large scale quantitation strategies (Label-free, SILAC, iTRAQ, PRM, neucode).
5(Tu 3rd) JM Posttranslational modifications: Protein vs peptide analysis. PTM enrichment, PTM cross-talk.
6(Th 5th) MT Architecture of protein complexes and machines (chemical cross-linking).

No need to register! Open to anyone! Free! Turn up only to the lectures you are interested in! Opportunity to analyze your own samples!

If you want to participate in either the lectures and/or the labs please email Al Burlingame, so that instructors can have an idea of the number of people who will attend.


ALB - Al Burlingame
RJC - Robert Chalkley
JM - Jason Maynard
JO - Juan Oses
MT - Mike Trnka
AU - Anatoly Urisman

National Institute of General Medical Sciences Adelson Medical Research Foundation