Quantitative Neuroproteomics

Closing date: TBC

Proteins are essential for biological function and understanding changes in the expression, modification and function of proteins is the goal of proteomics. Therefore, techniques and concepts that allow the direct measurement of how proteins change are vital for our continued understanding of human health and disease.  This course provides an overview of proteomics and the tools used to conduct proteomics with a particular emphasis on mass spectrometry.  Students will be encouraged to design a quantitative mass spectrometry-based assay for one of their favourite proteins using the Neuroproteomics Facility at the Florey.

Coursework: In-class quiz, design a discovery experiment relevant to your research to perform a database search on.

  1. The basics of proteins
    1. Know thy amino acids
    2. Structure and function relationships
    3. Post translation modifications (PTM)
      1. Covalent vs non-covalent
  2. Theory of Proteomics
    1. Anything a cell does a protein does it
    2. Concepts and promises that drive proteomics and personalized medicine.
  3. The biggest question in any protein lab; what’s the concentration?
    1. Amino acid analysis
    2. UV
    3. IR
    4. Chromophoric/fluorophoric based assays
  4. The practice of proteomics
    1. Tools of the trade
    2. Discovery vs targeted
      1. PAGE based assays (2D gels)
      2. Antibody based technology (e.g. ELISA, Proteins Arrays)
      3. Bottom-up and Top-down mass spectrometry
  5. It is all about mass-to-charge
    1. Q’s, TOFs, traps and magnets
    2. Ionization of proteins
    3. Resolution vs accuracy
  6. Fragmentation and database searching (statistics)
    1. Collision induced disassociation, electron transfer and capture…
    2. MASCOT, SEQUEST, Xtandem….
  7. Quantitative mass spectrometry of proteins
    1. Accurate mass and time
    2. Stable isotope dilution
    3. Isobaric tags and multiplexing
    4. Software (Skyline etc.)
  8. Post-translation modifications
    1. Covalent PTMomics (phosphomics, glycomics etc.)
    2. Non-covalent omics Metallomics
      1. LC-ICP-MS
      2. The advantage of stable Isotopes
    3. Interactomics
      1. Immunoprecipitations and cross-linking
  9. The current state of the art.
    1. Equipment
    2. Bottom-up vs top-down. Will there be a winner?


Dr Blaine Roberts and Dr Nick Williamson

Proposed timeframe:

Either Q3 (not September) or Q4 2018; exact time to be advised.


Two 1.5 hr lectures per week over 5-6 weeks plus hands-on activities in the laboratory.

Time Commitment:

18-20hrs contact time

Prerequisites: TBA