Publications by methodology
iTRAQ
Alice Chen Liang Len, Michael B Powner, Ling Zhu, Gregory S Hageman, Xiaomin Song, Marcus Fruttiger, and Mark C Gillies. Pilot application of iTRAQ to the retinal disease Macular Telangiectasia. J. Proteome Res., 2012, 11 (2), pp 537–553
Jianxin Yang, Margit L. MacDougall, Michael T. McDowell, Li Xi, Ru Wei, William J. Zavadoski, Mark P. Molloy, John D Baker, Max Kuhn, Over Cabrera, and Judith L.Treadway. Polyomic Profiling Reveals Significant Hepatic Metabolic Alterations in Glucagon-Receptor (GCGR) Knockout Mice: Implications on Anti-Glucagon Therapies for Diabetes. BMC Genomics 2011, 12:281, 1 June 2011
Zhao, L., Lee, B.Y., Brown, D.A., Molloy, M. P., Marx, G. M., Pavlakis, N., Boyer, M. J., Stockler, M. R., Kaplan, W., Breit, S. N., Sutherland, R. L., Henshall, S. M., Horvath, L. G. Identification of candidate biomarkers of therapeutic response to docetaxel by proteomic profiling. Cancer Res. 2009, 69 (19), 7696-7703.
V Rhein, X Song, A Wiesner, LM Ittner, G Baysang, F Meier, L Ozmen, H Bluethmann, S Drose, U Brandt, E Savaskan, C Czech, J Gotz, and A Eckert Amyloid-β and tau synergistically impair the oxidative phosphorylation system in triple transgenic Alzheimer’s disease mice, Proc Natl Acad Sci U S A. Nov 24, 2009; 106(47), 20057-62
Song, X, Bandow, J, Sherman, J, Baker, J.D., Brown, P.W., McDowell, M.T., Molloy, M.P. iTRAQ Experimental Design for Plasma Biomarker Discovery. J Proteome Res. 2008, 7, 2952-2958.
SILAC
Ali, N. and Molloy, M.P. Quantitative phosphoproteomics of transforming growth factor beta signaling in colon cancer cells. Proteomics 2011, 11, 3390-401. Cover Image
MRM
Randall, S.R., McKay, M.J., Molloy, M.P. Evaluation of blood collection tubes using selected reaction monitoring mass spectrometry: implications for proteomic biomarker studies. Proteomics. 2010 May;10(10):2050-6
Sherman, J., McKay, M. J., Ashman, K., Molloy, M. P. Unique ion signature Mass Spectrometry: a deterministic method to assign peptide identity. Mol. Cell. Proteomics. 2009, 8(9), 2051-2062.
Chiu, C. L., Randall, S., Molloy, M. P. Recent progress in selected reaction monitoring mass spectrometry driven plasma protein biomarker analysis. Bioanalysis, 2009, 1(4), 847-855.
Sherman, J., McKay, M. J., Ashman, K., Molloy, M. P. How specific is my SRM? The issue of precursor and product ion redundancy. Proteomics, 2009, 9, 1120-1123.
Other Mass Spec
Mehdi Mirzaei, Dana Pascovici, Brian J. Atwell and Paul A. Haynes. Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery. Proteomics 2012, 12, 864–877
McQuade, L.R., Schmidt, U., Pascovici, D., Stojanov, T., Baker, M.S. Improved membrane proteomics coverage of human embryonic stem cells by IPG-IEF. J Proteome Res. 2009, 8 (12), 5642-5649
Peterson, R., Grinyer, J., Joss, J., Khan, A., and Nevalainen, A.K.M. (2009). Fungal proteins with mannanase activity identified directly from a Congo Red stained zymogram using mass spectrometry. Journal of Microbiological Methods, 79:374-377.
Liaw T.Y., Salam N.K., McKay M.J., Cunningham A.M., Hibbs D.E., Kavallaris M., Class I beta-tubulin mutations in 2-methoxyestradiol-resistant acute lymphoblastic leukemia cells: implications for drug-target interactions. Mol. Cancer Ther. 2008; 7(10):3150-9.
Chick JM, Haynes PA, Bjellqvist B, Baker MS. A combination of immobilised pH gradients improves membrane proteomics. J Proteome Res. 2008 Nov;7(11):4974-81. Epub 2008 Oct 7. PubMed PMID: 18837535.
Chick JM, Haynes PA, Molloy MP, Bjellqvist B, Baker MS, Len AC. Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing. J Proteome Res. 2008
Protein-Protein Interactions
Sigglekow ND, Pangon L, Brummer T, Molloy M, Hawkins NJ, Ward RL, Musgrove EA, Kohonen-Corish MR. Mutated in Colorectal Cancer Protein Modulates the NFκB Pathway. Anticancer Res. 2012 Jan;32(1):73-9.
Saldanha RG, Xu N, Molloy MP, Veal DA, Baker MS. Differential proteome expression associated with urokinase plasminogen activator receptor (uPAR) suppression in malignant epithelial cancer. J Proteome Res. 2008 Nov;7(11):4792-806. Epub 2008 Sep 23. PubMed PMID: 18808175.
Protein Chemistry
Nigel K. Stepto, Benjamin B. Shipperd, Graeme Hyman, Bernie McInerney, and David B. Pyne. Effects of high-dose large neutral amino acid supplementation on exercise, motor skill, and mental performance in Australian Rules Football players. Appl. Physiol. Nutr. Metab. Vol. 36, 2011 671-681
Systems Biology
Cristian Varela, Simon A Schmidt, Anthony R Borneman, Jens O Krömer, Alamgir Khan, Paul J Chambers & The Australian Wine Yeast Systems Biology Consortium. Systems biology: a new paradigm for industrial yeast strain development. Microbiology Australia, In Focus November 2011 Pg 151-155
2D Gels
Natsuko Tokushige, Robert Markham, Ben Crossett, Seong B. Ahn, Vidya L. Nelaturi, Alamgir Khan, and Ian S. Fraser. Discovery of a novel biomarker in the urine in women with endometriosis. Fertility and Sterility, Volume 95 Issue 1, January 2011, pages 46-49
Polaskova, V, Kapur, A, Khan, A, Molloy, M.P., Baker, M.S. High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis. 2010 Jan;31(3):471-482.
Lam, F.F., Jankova, L, Dent, O.F., Molloy, M.P., Kwun, S.Y., Clarke, C, Chapuis, P, Robertson, G, Beale, P, Clarke, S, Bokey, E.L., Chan, C. Identification of distinctive protein expression patterns in colorectal adenoma. Proteomics Clin. Appl. 2010, 4, 60–70.
Khan, A., Williams, K.L., Soon, J. & Nevalainen, H. (2008). Proteomic analysis of the knob-producing nematode trapping fungus Monacrosporium lysipagum. Mycological Research, 112: 1447-1452.
Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P.A., Borthwick, A., Cash, P., Day, B.W., Friedman, D.B., Garland, D., Gutstein, H.B., Hoogland, C., Jones, N.A., Jones, A.R., Khan, A., Klose, J., Lamond, A.I., Lemkin, P.F., Lilley, K.S., Minden, J., Morris, N.J., Paton, N.W., Pisano, M.R., Prime, J.E., Rabilloud, T., Stead, D.A., Taylor, C.F., Voshol, H., and Wipat, A. (2008). MIPAE: Gel electrophoresis. Nature Biotechnology, 26(8): 863-864.
Bioinformatics
Dana Pascovici, Tim Keighley, Mehdi Mirzaei, Paul A. Haynes and Brett Cooke.PloGO: Plotting gene ontology annotation and abundance in multi-condition proteomics experiments. Proteomics 2012, 12, 406–410
Mirzaei M, Soltani N, Sarhadi E, Pascovici D, Keighley T, Salekdeh GH, Haynes PA, Atwell BJ. Shotgun proteomic analysis of long-distance drought signaling in rice roots. J Proteome Res. 2012 Jan 1;11(1):348-58. Epub 2011 Dec 2
Gammulla CG, Pascovici D, Atwell BJ, Haynes PA. Differential proteomic response of rice (Oryza sativa) leaves exposed to high- and low-temperature stress. Proteomics. 2011 Jul;11(14):2839-50. doi: 10.1002/pmic.201100068. Epub 2011 Jun 22.
Mehdi Mirzaei, Dana Pascovici, Tim Keighley, Iniga George, Claudia Voelckel, Peter B. Heenan, Paul A. Haynes. Shotgun proteomic profiling of five species of New Zealand Pachycladon. PROTEOMICS Volume 11, Issue 1, pages 166-171, No. 1 January 2011
Gammulla CG, Pascovici D, Atwell BJ, Haynes PA. Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low-temperature stress. Proteomics. 2010 Aug;10(16):3001-19. PubMed PMID: 20645384.
Voelckel C, Mirzaei M, Reichelt M, Luo Z, Pascovici D, Heenan PB, Schmidt S, Janssen B, Haynes PA, Lockhart PJ. Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon. BMC Evol Biol. 2010 May 20;10:151. PubMed PMID: 20482888; PubMed Central PMCID: PMC2886070.
Bioplex Assays
M. Nalos, M., Huang, S., Sluyter, R., Khan, A., Santner-Nanan, B., Nanan, R. and McLean, A.S. (2008). “Host tissue damage” signal ATP impairs IL-12 and IFNg secretion in LPS stimulated whole human plasma. Journal of Intensive Care Medicine, 34: 1891-1897.
Glycoproteomic Analysis
Lee A, Chick JM, Kolarich D, Haynes PA, Robertson GR, Tsoli M, Jankova L, Clarke SJ, Packer NH, Baker MS. Liver Membrane Proteome Glycosylation Changes in Mice Bearing an Extra-hepatic Tumor. Mol Cell Proteomics. 2011 Sep;10(9):
Sumer-Bayraktar Z, Kolarich D, Campbell MP, Ali S, Packer NH, Thaysen-Andersen M. N-glycans modulate the function of human corticosteroid-binding globulin. Mol Cell Proteomics. 2011 Aug;10(8):M111.009100. Epub 2011 May 10.
Parker BL, Palmisano G, Edwards AV, White MY, Engholm-Keller K, Lee A, Scott NE, Kolarich D, Hambly BD, Packer NH, Larsen MR, Cordwell SJ. Quantitative N-linked glycoproteomics of myocardial ischemia and reperfusion injury reveals early remodeling in the extracellular environment. Mol Cell Proteomics. 2011 Aug;10(8):M110.006833. Epub 2011 Mar 25.
Graham ME, Thaysen-Andersen M, Bache N, Craft GE, Larsen MR, Packer NH, Robinson PJ. A novel post-translational modification in nerve terminals: O-linked N-acetylglucosamine phosphorylation. J Proteome Res. 2011 Jun 3;10(6):2725-33. Epub 2011 May 2.
Scott NE, Parker BL, Connolly AM, Paulech J, Edwards AV, Crossett B, Falconer L, Kolarich D, Djordjevic SP, Højrup P, Packer NH, Larsen MR, Cordwell SJ. Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni. Mol Cell Proteomics. 2011 Feb;10(2):M000031-MCP201. Epub 2010 Apr 1.
Lee A, Nakano M, Hincapie M, Kolarich D, Baker MS, Hancock WS, Packer NH. The lectin riddle: glycoproteins fractionated from complex mixtures have similar glycomic profiles. OMICS. 2010 Aug;14(4):487-99.
Deshpande N, Jensen PH, Packer NH, Kolarich D. GlycoSpectrumScan: fishing glycopeptides from MS spectra of protease digests of human colostrum sIgA. J Proteome Res. 2010 Feb 5;9(2):1063-75.
Wada Y, Dell A, Haslam SM, Tissot B, Canis K, Azadi P, Bäckström M, Costello CE, Hansson GC, Hiki Y, Ishihara M, Ito H, Kakehi K, Karlsson N, Hayes CE, Kato K, Kawasaki N, Khoo KH, Kobayashi K, Kolarich D, Kondo A, Lebrilla C, Nakano M, Narimatsu H, Novak J, Novotny MV, Ohno E, Packer NH, Palaima E, Renfrow MB, Tajiri M, Thomsson KA, Yagi H, Yu SY, Taniguchi N. Comparison of methods for profiling O-glycosylation: Human Proteome Organisation Human Disease Glycomics/Proteome Initiative multi-institutional study of IgA1.Mol Cell Proteomics. 2010 Apr;9(4):719-27. Epub 2009 Dec 28.
Jensen PH, Kolarich D, Packer NH. Mucin-type O-glycosylation--putting the pieces together. FEBS J. 2010 Jan;277(1):81-94. Epub 2009 Nov 17.
Lee A, Kolarich D, Haynes PA, Jensen PH, Baker MS, Packer NH. Rat liver membrane glycoproteome: enrichment by phase partitioning and glycoprotein capture. J Proteome Res. 2009 Feb;8(2):770-81. PubMed PMID: 19125615.