Professor Mark Baker

Professor Mark BakerProfessor of Proteomics

BSc(Hons), PhD (Macquarie University)

Contact Details

Tel: +61 (0)2 9850 8211



Professional Overview

Professor Baker obtained a BSc(Hons) (1981) and PhD (1985) in biochemistry from Macquarie University investigating oxidation of proteins in vitro and extending this to in vivo human disease situations. He has been CEO and Director of APAF, building it into a competitive well-funded national NCRIS infrastructure facility and Director of the Biomolecular Frontiers Research Centre at Macquarie University. He has primarily been responsible for making Macquarie a centre of proteomics excellence for more than a decade. He is now a major driver scientifically and managerially of the global Human Protein Project (HPP). He convened HUPO2010 at which the HPP was launched. He is managing the Chr7 HPP and Human Plasma HPP projects and is on the HUPO and HPP Executive Committee. Prof Baker has established an international reputation in fields related to proteomics, protein structure and function oxidation of proteins, serine proteases/receptors/inhibitors and membrane proteomics). This is evidenced by a 2012 HUPO Distinguished Service Award and three  patents, 120 peer reviewed publications and a h index=30, positions on editorial boards, international Congress plenary invitations, HUPO Board and recently Executive Committee election and successful supervision of  40 postgraduates.

Current Research Overview

Prof Bakers current research interests cover cancer proteomics, biomarkers and molecular cell biology, including; advanced proteomic technologies, cancer metastasis and how portease receptors, growth factor receptors and integrins membrane protein networks regulate the pathobiology of cancer.  These include the development of novel platforms to determine what and how proteins interact to regulate metastasis and early cancer blood protein biomarker discovery.  He is the current chair of the HUPO Plasma Proteome Project and is coordinator of a number of Australian/NZ efforts in the chromosomal and biology/disease 'pillars' of the global Human Proteome Project (HPP).  Prof Baker also has active collaborations with scientists in Australia, NZ, USA, Sweden, Spain, Switzerland, China, Germany and Japan.

Select Research Grants (last five years)

  • 2006-11 Baker MS. Proteomics Australia Consortium, NCRIS Scheme Funding ~$28M
  • 2007-11 Clarke S, Bokey EL , Baker MS, et al, Novel protein biomarkers for improving colorectal cancer therapy (NSW Cancer Institute Translational Grant), 5yrs, $3,750,000.
  • 2007-2010 Baker MS, Packer N, Robinson P, Clarke S, et al., NSW Cancer Institute Infrastructure: Cancer Glycoproteomics Initiative), $1,065,459.
  • 2008 Dawes IW, Bergquist PL, Trent RJ, Scott RJ, Hogg PJ, Wilkins MR, Reichardt JKV, Hunt NH, Baker MS, Dunkley PR. Advanced high throughput functional genomics and gene mapping. ARC LIEF. LE0882512. $400,000.
  • 2008-10 Baker MS, Molloy M. Saldanha R, (Cancer Council NSW, Project Grant) Lynchpin protein interactions that drive epithelial malignancy; $300,000.
  • 2009 Robinson, Baker MS et al., A Mass Spectrometer for NSW Cancer Phosphoproteomics Research (NSW Cancer Institute Equipment Grant), $300,000.
  • 2010-2 Clarke S, Robertson G, Piquette-Miller M, McLachlan A, Baker MS, Katsifis A. Improving the use of chemotherapy by targeting the inflammatory response NHMRC Project Grant 632848 $550,500.
  • 2010 Packer NH, Robinson PJ, von Itzstein M, et al., Baker MS, Reddel RR. Beyond Proteomics: structure and function of protein modifications ARC LIEF, $500,000.
  • 2010-11Baker MS, He F, Hancock W, Molloy MP, Clarke S. Wilkins MR, Packer NH. NSW:China Collaborative Grant: Cancer Genesis, Spread & Treatment Proteomic Discovery Program NSW Gov't. total $250,000.
  • 2010-2 Baker MS & Nice E. A Colo "Interactome" Paradigm that Influences Patient Survival Cancer Council NSW Project Grant Application #604016, 3yrs, total $300,000.
  • 2011-3 Inglis DW, Goldys EM, Baker MS, Calander NP, Austin RH, ARC Discovery Project DP110102207, Quest for trace biomarkers in complex media through innovative nanoscale science of fluids, molecules, particles and light.; 3yrs, total $300,000pa.
  • 2011-3 Baker, MS and Nice, E. Colorectal Cancer Membrane Protein Interactomics [A Major Discriminator of Clinical Outcome] NHMRC Project Grant. Total $621,732.
  • 2012 Baker, MS. NHMRC Standard Equipment Grant; Perkin Elmer JANUS robotic IP system, $12,438 (NHMRC), $2,562 (MQ).
  • 2013 Baker, MS, Ranganathan S and Nice, E. Membrane Protein Interactomics Determine the Paradoxical Cancer Biology of TGFb. MQ (NHMRC) Safety Net Grant, $25,000.

Five Select Research Publications

  1. Lee, A, Kolarich D, Haynes PA, Packer, NH, Baker, MS. Liver Membrane Proteome Glycosylation Changes in Mice Bearing an Extrahepatic Tumor. Mol. Cell Proteomics, Sep;10(9): M900538MCP200, 2011; [IF = 8.8].
  2. Jankova L, Chan C, Fung CL, Song X, Kwun SY, Cowley M, Kaplan W, Dent OF, Bokey L, Chapuis PH, Baker MS, Robertson GR, Clarke SJ, Molloy MP. Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry, Mol. BioSyst., 2011, 7, 2997-3005.
  3. Cantor D, Slapetova I, Kan A, McQuade LR and Baker MS Overexpression of αvβ6 integrin alters the colorectal cancer cell proteome in favour of elevated proliferation and a switching in cellular adhesion which increases invasion. J Proteome Res. 2013 Jun 7; 12(6):2477-90. doi: 10.1021/pr301099f. [IF = 5.1].
  4. Sethi MK, Thaysen-Andersen M, Smith JT, Baker MS, Packer NH, Hancock WS, Fanayan S. Comparative N-Glycan Profiling of Colorectal Cancer Cell Lines Reveals Unique Bisecting GlcNAc and α-2,3-Linked Sialic Acid Determinants Are Associated with Membrane Proteins of the More Metastatic/Aggressive Cell Lines. J Proteome Res. 2013 Dec 2.  PMID: 24295106. [IF = 5.1].
  5. Gopichandran S, Khan JM, Anand S, Ahn SB, Baker MS, Ranganathan S. A site for direct integrin αvβ6uPAR interaction from structural modelling and docking. J. Structural Biol. J Struct. Biol. 2014 Jan 11. pii: S1047-8477(14)00002-1. doi: 10.1016/j.jsb.2014.01.001. [IF = 3.36].


Current Staff

Dr Fei Liu, Senior Lecturer (CBMS, MQ)
Functional chemical biology of human claudin family proteins

Dr Susan Fanayan, Senior Research Fellow
Interactions of driver oncogenes located in different chromosomes -role of ERBB2 (chr.17), EGFR (chr.7) and MYC (chr.8); Breast, medulloblastoma and colon cancer onco"omics"; Characterizing human olfactory receptors

Dr Charlie (Seong Beom) Ahn, Research Fellow
The role of membrane uPAR v6 interactomics in colorectal cancer metastasis

Dr Abidali Mohamedali, Research Fellow (CBMS,MQ)
In search of the Human Proteome Project's "Missing Proteins"

Current Students

Ms Sadia Mahboob, PhD HDR student
Deep discovery of candidate CRC clinical stage biomarkers

Mr David Cantor, PhD HDR student
Thesis title: Role of the avβ6 integrin in promoting colorectal cancer metastasis

Ms Nurul Jufri, PhD HDR student
Thesis title: Proteomic analysis on the effect of estrogen and tensile stretch to human cerebral vascular endothelial cells

Mr Harish R Cheruku, PhD HDR student

Thesis title: Transforming Growth Factor-β associated membrane proteomics in colorectal cancer cells

Ms Bhooma Venkatraman, PhD HDR student
Membrane proteomic biomarkers of triple negative breast cancer