Publications 2012 and Prior years

2012

Randall, S A; McKay, M J; Pascovici, D; Mahon, K; Horvath, L; Clarke, S J; Molloy, M P. Remarkable temporal stability of high-abundance human plasma proteins assessed by targeted mass spectrometry. Proteomics Clin. Appl. 2012 Dec; 6(11-12): 626-34.

Su SP, Lyons B, Friedrich M, McArthur JD, Song X, Xavier D, Truscott RJ, Aquilina JA.  Molecular signatures of long-lived proteins:  autolytic cleavage adjacent to serine residues.  Aging Cell. 2012 Dec;11(6):1125-7.

Nicholson, J; Neelagandan, K; Huart, A-S; Ball, K; Molloy, M P; Hupp, T. An iTRAQ proteomics screen reveals the effects of the MDM2 binding ligand Nutlin-3 on cellular proteostasis. J. Proteome. Res. 2012 Nov 2: 11(11): 5464-78.

Kho, P S S; Jankova, L; Fung, C L-S; Chan, C; Clarke, C; Lin, B P C; Robertson, G; Molloy, M; Chapuis, P H; Bokey, E L; Dent, O F; Clarke, S. Overexpression of protein S100A4 is independently associated with overall survival in stage C colonic cancer but only in cytoplasm at the advancing tumour front. Int. J. Colorectal Dis. 2012 Nov; 27(11):1409-17.

Simonian, M; Molloy, M P; Stoodley, M A. In Vitro and In Vivo Biotinylation of Endothelial Cell Surface Proteins in the Pursuit of Targets for Vascular Therapies for Brain AVMs. Metabolomics 2012, S1:007.

Blaber, S P; Webster, R A; Hill, C J; Breen, E J; Kuah, E; Vesey, G; Herbert, B R. Analysis of in vitro secretion profiles from adipose derived cell populations. J. Transl. Med. 2012 Aug 22; 10:172.

Khan, A. Detection and quantitation of forty eight cytokines, chemokines, growth factors and nine acute phase proteins in healthy human plasma, saliva and urine. J. Proteomics. 2012 Aug 3;75(15): 4802-19.

Jankova, L; Robertson, G; Chan, C; Tan, K L; Kohonen-Corish, M; Fung, C L-S; Clarke, C; Lin, B P C; Molloy, M; Chapuis, P H; Bokey, L; Dent, O F; Clarke, S J. Glutathione S-transferase Pi Expression Predicts Response to Adjuvant Chemotherapy for Stage C Colon Cancer: a Matched Historical Control Study. BMC Cancer 2012 May 28; 12:196.

Sherman, J; Molloy, M P; Burlingame, A L. Why complexity and entropy matter: Information, Post-Translational Modifications, and Assay Fidelity. Proteomics 2012 Apr; 12(8): 1147-50.

Mirzaei, M; Pascovici, D; Atwell, B J and Haynes, P A. Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery. Proteomics 2012 Mar; 12(6): 864-77.

Pascovici, D; Keighley, T; Mirzaei, M; Haynes, P A; Cooke, B. PloGO: Plotting gene ontology annotation and abundance in multi-condition proteomics experiments.  Proteomics 2012 Feb; 12(3): 406-10.

Krisp, C; McKay, M J; Wolters, D A; Molloy, M P. MudPIT-SRM improves detection and quantification for protein biomarker studies. Anal. Chem. 2012 Feb 7; 84(3): 1592-600.

Len, A C L; Powner, M B; Zhu, L; Hageman, G S; Song, X; Fruttiger, M; Gillies. M C. Pilot application of iTRAQ to the retinal disease Macular Telangiectasia. J. Proteome Res. 2012 Feb 3; 11(2): 537-53.

Schmidt, S A; Jacob, S S; Ahn, S B; Rupasinghe, T; Krömer, T J; Khan, A; Varela, C. Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast. Metabolomics 2013 Feb; 9(1): 173-88.

Mirzaei, M; Soltani, N; Sarhadi, E; Pascovici, D; Keighley, T; Salekdeh, G H; Haynes, P A; Atwell, B J. Shotgun proteomic analysis of long-distance drought signaling in rice roots.  J Proteome Res. 2012 Jan 1;11(1):348-58.

Sigglekow, N D; Pangon, L; Brummer, T; Molloy, M; Hawkins, N J; Ward, R L; Musgrove, E A; Kohonen-Corish, M R. Mutated in colorectal cancer protein modulates the NFκB pathway. Anticancer Res. 2012 Jan; 32(1):73-9.

Krisp, C; Randall, S; McKay, M J; Molloy, M P. Towards clinical applications of selected reaction monitoring for plasma protein biomarker studies. Proteomics Clin. Appl. 2012 Jan; 6(1-2): 42-59.

Sharma, M; Jamieson, C; Johnson, M; Molloy, M P; Henderson, B R. Specific armadillo repeat sequences facilitate beta-catenin nuclear transport in live cells via direct binding to nucleoporins Nup62, Nup153 and RANBP2/Nup358 . J. Biol. Chem. 2012 Jan 6, 287(2), 819-31.

2011

Tan, K L; Jankova, L; Chan, C; Fung, C L; Clarke, C; Lin, B P; Robertson, G R; Molloy, M P; Chapuis P H; Bokey, L; Dent, O F; Clarke, S J. Clinicopathological correlates and prognostic significance of glutathione s-transferase pi expression in 468 patients after potentially curative resection of node-positive colon cancer. Histopathology 2011 Dec; 59(6): 1057-70.

Varela, C; Schmidt, S A; Borneman, A R; Krömer, J O; Khan, A; Chambers, P J and The Australian Wine Yeast Systems Biology Consortium. Systems biology: a new paradigm for industrial yeast strain development. Microbiology Australia, In Focus November 2011: 151-155

Jankova, L; Chan, C; Fung, C L S; Song, X; Kwun, S Y; Cowley, M J; Kaplan, W; Dent, O F; Bokey, E L; Chapuis, P H; Baker, M S; Robertson, G R; Clarke, S J; Molloy, M P. Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry. Mol. Biosystems 2011 Nov; 7(11): 2997-3005.

Stepto, N K; Shipperd, B B; Hyman, G; McInerney, B; Pyne, D B. 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. 2011 Oct; 36(5): 671-81.

Lee, A; Chick, J M; Kolarich, D; Haynes, P A; Robertson, G R; Tsoli, M; Jankova, L; Clarke, S J; Packer, N H; Baker, M S. Liver Membrane Proteome Glycosylation Changes in Mice Bearing an Extra-hepatic Tumor. Mol Cell Proteomics. 2011 Sep; 10(9):M900538MCP200.

Fung, D C; Lo, A; Jankova, L; Clarke, S J; Molloy, M; Robertson, G R; Wilkins, M R.  Classification of cancer patients using pathway analysis and network clustering.  Methods Mol Biol. 2011;781:311-36.

Ali, N A; Molloy, M P.  Quantitative phosphoproteomics of transforming growth factor-beta signaling in colon cancer cells.  Proteomics. 2011 Aug; 11(16): 3390-401

Sumer-Bayraktar, Z; Kolarich, D; Campbell, M P; Ali, S; Packer, N H; Thaysen-Andersen, M. N-glycans modulate the function of human corticosteroid-binding globulin. Mol Cell Proteomics. 2011 Aug;10(8):M111.009100.

Parker, B L; Palmisano, G; Edwards, A V; White, M Y; Engholm-Keller, K; Lee, A; Scott, N E; Kolarich, D; Hambly, B D; Packer, N H; Larsen, M R; Cordwell, S J. 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.

Gammulla, C G; Pascovici, D; Atwell, B J; Haynes, P A. Differential proteomic response of rice (Oryza sativa) leaves exposed to high- and low-temperature stress.  Proteomics. 2011 Jul;11(14):2839-50.

Dolai, S; Xu, Q; Liu, F; Molloy, M P.  Quantitative chemical proteomics in small-scale culture of phorbol ester stimulated basal breast cancer cells.  Proteomics 2011 Jul; 11(13): 2683-92.

Graham, M E; Thaysen-Andersen, M; Bache, N; Craft, G E; Larsen, M R; Packer, N H; Robinson, P J. A novel post-translational modification in nerve terminals: O-linked N-acetylglucosamine phosphorylation. J Proteome Res. 2011 Jun 3; 10(6):2725-33.

Yang, J; MacDougall, M L; McDowell, M T; Xi, L; Wei, R; Zavadoski, W J; Molloy, M P; Baker, J D; Kuhn, M; Cabrera, O; Treadway, J L. Polyomic Profiling Reveals Significant Hepatic Metabolic Alterations in Glucagon-Receptor (GCGR) Knockout Mice. BMC Genomics. 2011 Jun 1; 12:281.

Scott, N E; Parker, B L; Connolly, A M; Paulech, J; Edwards, A V; Crossett, B; Falconer, L; Kolarich, D; Djordjevic, S P; Højrup, P; Packer, N H; Larsen, M R; Cordwell, S J. 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.

Mirzaei, M; Pascovici, D; Keighley, T; George, I; Voelckel, C; Heenan, P B; Haynes, P A. Shotgun proteomic profiling of five species of New Zealand Pachycladon.  Proteomics 2011 Jan; 11(1): 166-71.

Tokushige, N; Markham, R; Crossett, B; Ahn, S B; Nelaturi, V L; Khan, A; Fraser, I S.  Discovery of a novel biomarker in the urine in women with endometriosis.  Fertility and Sterility. 2011 Jan; 95(1):46-9.

2010

Randall, S R; McKay, M J; Baker, M S; Molloy, M P.  Evaluation of blood collection tubes using selected reaction monitoring mass spectrometry: implications for proteomic biomarker studies.  Proteomics. 2011 Dec;11(23):4593.

Ali, N A; McKay. M J; Molloy, M P. Proteomics of Smad4 regulated transforming growth factor-beta signalling in colon cancer cells. Mol Biosyst. 2010 Nov;6(11):2332-8.

Gammulla, C G; Pascovici, D; Atwell, B J; Haynes, P A. Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low-temperature stress. Proteomics. 2010 Aug;10(16):3001-19.

Lee, A; Nakano, M; Hincapie, M; Kolarich, D; Baker, M S; Hancock, W S; Packer, N H. The lectin riddle: glycoproteins fractionated from complex mixtures have similar glycomic profiles. OMICS. 2010 Aug;14(4):487-99.

Voelckel, C; Mirzaei, M; Reichelt, M; Luo, Z; Pascovici, D; Heenan, P B; Schmidt, S; Janssen, B; Haynes, P A; Lockhart, P J. Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon. BMC Evol Biol. 2010 May 20;10:151.

Wada, Y; Dell, A; Haslam, S M; Tissot, B; Canis, K; Azadi, P; Bäckström, M; Costello, C E; Hansson, G C; Hiki, Y; Ishihara, M; Ito, H; Kakehi, K; Karlsson, N; Hayes, C E; Kato, K; Kawasaki, N; Khoo, K H; Kobayashi, K; Kolarich, D; Kondo, A; Lebrilla, C; Nakano, M; Narimatsu, H; Novak, J; Novotny, M V; Ohno, E; Packer, N H; Palaima, E; Renfrow, M B; Tajiri, M; Thomsson, K A; Yagi, H; Yu, S Y; 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.

Deshpande, N; Jensen, P H; Packer, N H; 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.

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):471-82.

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 Jan; 4(1): 60–70.

2009

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 Dec; 8(12): 5642-9.

Peterson, R; Grinyer, J; Joss, J; Khan, A; Nevalainen, A K M. Fungal proteins with mannanase activity identified directly from a Congo Red stained zymogram using mass spectrometry. Journal of Microbiological Methods. 2009 Dec;79(3):374-7.

Rhein, V; Song, X; Wiesner, A; Ittner, L M; Baysang, G; Meier, F; Ozmen, L; Bluethmann, H; Drose, S; Brandt, U; Savaskan, E; Czech, C; Gotz, J; Eckert, A. Amyloid-β and tau synergistically impair the oxidative phosphorylation system in triple transgenic Alzheimer’s disease mice,  Proc Natl Acad Sci USA. 2009 Nov 24; 106(47): 20057-62

Chua, W; Randall, S; McKay, M J; Horvath, L; Clarke, S J; Molloy, M P.  Plasma biomarkers for early prediction of chemotherapy response and toxicity in colorectal cancer.  EJC Supplements. 2009, 7 (2) 112-112

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 Oct 1; 69 (19): 7696-703.

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 Sep, 8(9): 2051-62

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Chiu, C L; Randall, S; Molloy, M P. Recent progress in selected reaction monitoring mass spectrometry driven plasma protein biomarker analysis. Bioanalysis, 2009 Jul; 1(4): 847-55.

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 Mar; 9(5): 1120-3.[Top 20 most viewed article 07/08-06/09].

Lee, A; Kolarich, D; Haynes, P A; Jensen, P H; Baker, M S; Packer, N H. Rat liver membrane glycoproteome: enrichment by phase partitioning and glycoprotein capture. J Proteome Res. 2009 Feb;8(2):770-81..  

Jensen, P H; Kolarich, D; Packer, N H. Mucin-type O-glycosylation--putting the pieces together. FEBS J. 2010 Jan;277(1):81-94.

2008

Khan, A; Williams, K L; Soon, J; Nevalainen, H.. Proteomic analysis of the knob-producing nematode trapping fungus Monacrosporium lysipagum. Mycological Research, 2008 Dec;112(pt 12): 1447-52.

Saldanha, R G; Xu, N; Molloy, M P; Veal, D A; Baker, M S. Differential proteome expression associated with urokinase plasminogen activator receptor (uPAR) suppression in malignant epithelial cancer. J Proteome Res. 2008 Nov;7(11):4792-806.

Chick, J M; Haynes, P A; Bjellqvist, B; Baker, M S. A combination of immobilised pH gradients improves membrane proteomics. J Proteome Res. 2008 Nov;7(11):4974-81.

Nalos, M; Huang, S; Sluyter, R; Khan, A; Santner-Nanan, B; Nanan, R; McLean, A S. “Host tissue damage” signal ATP impairs IL-12 and IFNg secretion in LPS stimulated whole human blood. Journal of Intensive Care Medicine, 2008 Oct; 34(10): 1891-7.

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 Oct; 7(10):3150-9.

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; Wipat, A. Jones, A R. MIAPE: Guidelines for reporting the use of gel electrophoresis in proteomics. Nature Biotechnology, 2008 Aug; 26(8): 863-4.

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 Jul; 7(7): 2952-8.

Chick, J M; Haynes, P A; Molloy, M P; Bjellqvist, B; Baker, M S; Len, A C.  Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing. J Proteome Res. 2008 Mar;7(3):1036-45.