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Biomedical Proteomics

Biomedical Proteomics

Mass Spectrometry (MS) is an extremely powerful analytical technique that underpins all modern day biomolecular science, making MS a valuable tool in understanding the causes of disease. 

Cellular life is made up of millions of unique molecules. MS measures the mass of molecules, facilitating the identification and characterization of key components in biological processes (proteins, carbohydrates, DNA, metabolites). MS can also define the signalling events that drive biological processes by identifying post-translational modifications (e.g. protein phosphorylation).

Proteomics is the ability to study proteins in our cells and tissues on a large scale as well as one at a time. Biomedical Proteomics at CMRI uses Liquid Chromatography–Tandem Mass Spectrometry (LC–MS/MS) to obtain information on the proteome from biological samples.

The facility supports CMRI and the Westmead Research Hub, as well as collaborations with external groups and individuals. The facility offers access to equipment and advice on feasibility, methodology and data analysis.

Biomedical Proteomics Facility
Biomedical Proteomics Facility


Untargeted proteomics and phosphoproteomics are the two main services performed at the facility using highly developed workflows that offer high depth of analysis. We also perform targeted protein analyses, custom protein analyses and custom metabolite analyses. Please contact us to discuss your project.

LC-MS/MS systems at the Biomedical Proteomics Facility:

Two Thermo Q Exactive Plus quadrupole-orbitrap systems enable rapid and confident identification and quantitation of proteins and posttranslational modifications. This highly sensitive work horse equipment enables high depth of proteome analysis and is compatible with the Tandem Mass Tag (TMT) multiplexing technology.

Multiple equipment items to support LC-MS/MS:

A Dionex UltiMate 3000 HPLC system supports multiple off-line chromatography workflows with ultraviolet peptide detection and fraction collection to allow greater depth of proteome analysis.

A Laser Puller Sutter Instrument P-2000 and Nanobaume capillary column packer allow the production of nano-flow chromatography columns with a pulled tip. This allows zero dead volume between the chromatography material and the electrospray emitter, which enables very high-resolution chromatography and sensitive LC-MS/MS detection.

Two Barocyclers are available to process multiple samples at high pressure to speed up and standardise sample preparation steps involving tissue solubilisation and digestion.

Independent use or full service:

The facility offers training so that researchers can become independent users of the MS equipment and use the adjoining wet laboratory space. The facility also offers full-service analysis of samples from lysis to LC-MS/MS and data processing. We partner with bioinformaticians to ensure quality outcomes.

If you believe an MS-based proteomics approach is suitable for your research, please discuss your needs with facility staff.

Dr Mark Graham, Lead Scientist

Dr Mark Graham

Dr Graham has over 20 years of experience in proteomics and specialises in phosphoproteomics.

Contact email:
[email protected] 

Facility Located at: Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW

Selected Recent Biomedical Proteomics Facility Publications

Müller, J. A., J. Betzin, J. Santos-Tejedor, A. Mayer, A. M. Oprişoreanu, K. Engholm-Keller, I. Paulußen, P. Gulakova, T. D. McGovern, L. J. Gschossman, E. Schönhense, J. R. Wark, A. Lamprecht, A. J. Becker, A. J. Waardenberg, M. E. Graham, D. Dietrich, and S. Schoch. "A Presynaptic Phosphosignaling Hub for Lasting Homeostatic Plasticity." Cell Rep 39, no. 3 (Apr 19 2022): 110696.

Fernando, M., S. Lee, J. R. Wark, D. Xiao, B. Y. Lim, M. O'Hara-Wright, H. J. Kim, G. C. Smith, T. Wong, E. T. Teber, R. R. Ali, P. Yang, M. E. Graham, and A. Gonzalez-Cordero. "Differentiation of Brain and Retinal Organoids from Confluent Cultures of Pluripotent Stem Cells Connected by Nerve-Like Axonal Projections of Optic Origin." Stem Cell Reports (Apr 19 2022).

Almazi, J. G., M. Alomari, L. Belov, O. G. Best, Y. Shen, M. E. Graham, S. P. Mulligan, and R. I. Christopherson. "Fludarabine Nucleoside Induces Major Changes in the P53 Interactome in Human B-Lymphoid Cancer Cell Lines." Nucleosides Nucleotides Nucleic Acids (Dec 10 2021): 1-7.

Fan, X., V. P. Masamsetti, J. Q. Sun, K. Engholm-Keller, P. Osteil, J. Studdert, M. E. Graham, N. Fossat, and P. P. Tam. "Twist1 and Chromatin Regulatory Proteins Interact to Guide Neural Crest Cell Differentiation." Elife 10 (Feb 8 2021).

Fan, X., A. J. Waardenberg, M. Demuth, P. Osteil, J. Sun, D. A. F. Loebel, M. Graham, P. P. L. Tam, and N. Fossat. "Twist1 Homodimers and Heterodimers Orchestrate Lineage-Specific Differentiation." Mol Cell Biol (Mar 16 2020).

Engholm-Keller, K., A. J. Waardenberg, J. A. Muller, J. R. Wark, R. N. Fernando, J. W. Arthur, P. J. Robinson, D. Dietrich, S. Schoch, and M. E. Graham. "The Temporal Profile of Activity-Dependent Presynaptic Phospho-Signalling Reveals Long-Lasting Patterns of Poststimulus Regulation." PLoS Biol 17, no. 3 (Mar 2019): e3000170.

Engholm-Keller, Kasper, Nicolai Bache, Sushma R. Rao, Jesse R. Wark, Martin R. Larsen, Phillip J. Robinson, and Mark E. Graham. "Affinity Proteomics for Interactome and Phosphoproteome Screening in Synaptosomes." In Synaptosomes. Edited by Kathryn M. Murphy. New York, NY: Springer New York, 2018.

Graham, M. E., M. F. Lavin, and S. V. Kozlov. "Identification of Atm Protein Kinase Phosphorylation Sites by Mass Spectrometry." Methods Mol Biol 1599 (2017): 127-44.

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