APAF Staff Publications by Year

APAF Staff Publications by Year


Steffen, P., Krisp, C., Yi, W., Yang, P., Molloy, M. P., & Schlüter, HMulti-laboratory analysis of the variability of shipped samples for proteomics following non-cooled international transport Analytical Biochemistry 10.1016/j.ab.2018.02.026

Scott, C., de Souza, F.F., Aristizabal, V.H.V., Hethrington, L., Krisp, C., Molloy, M., Baker, M.A., Dell'Aqua, J.A.Proteomic profile of sex-sorted bull sperm evaluated by SWATH-MS analysis Animal Reproduction Science 10.1016/j.anireprosci.2018.09.010

Noor, Zainab; Wu, Jemma X; Pascovici, Dana; Mohamedali, Abidali; Molloy, Mark P; Baker, Mark S; Ranganathan, Shoba; Wren, Jonathan; "iSwathX: an interactive web-based application for extension of DIA peptide reference libraries Bioinformatics 10.1093/bioinformatics/bty660

Krisp, C., Parker, R., Pascovici, D., Hayward, N.K., Wilmott, J.S., Thompson, J.F., Mann, G.J., Long, G.V., Scolyer, R.A., Molloy, M.P.Proteomic phenotyping of metastatic melanoma reveals putative signatures of MEK inhibitor response and prognosis British Journal of Cancer 10.1038/s41416-018-0227-2

Lee, A., Rayner, S.L., Gwee, S.S.L., De Luca, A., Shahheydari, H., Sundaramoorthy, V., Ragagnin, A., Morsch, M., Radford, R., Galper, J., Freckleton, S., Shi, B., Walker, A.K., Don, E.K., Cole, N.J., Yang, S., Williams, K.L., Yerbury, J.J., Blair, I.P., Atkin, J.D., Molloy, M.P., Chung, R.S.Pathogenic mutation in the ALS/FTD gene, CCNF, causes elevated Lys48-linked ubiquitylation and defective autophagy Cellular and Molecular Life Sciences 10.1007/s00018-017-2632-8

Abbasi, M., Gupta, V., Chitranshi, N., You, Y., Dheer, Y., Mirzaei, M., Graham, S.L.Regulation of brain-derived neurotrophic factor and growth factor signaling pathways by tyrosine phosphatase Shp2 in the retina: A brief review Frontiers in Cellular Neuroscience 10.3389/fncel.2018.00085

Bhatnagar, A., McKay, M.J., Crumbaker, M., Ahire, K., Karuso, P., Gurney, H., Molloy, M.P.Quantitation of the anticancer drug abiraterone and its metabolite ?(4)-abiraterone in human plasma using high-resolution mass spectrometry Journal of Pharmaceutical and Biomedical Analysis 10.1016/j.jpba.2018.03.012

Lin, C.-H., Krisp, C., Packer, N.H., Molloy, M.P.Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge Journal of Proteomics 10.1016/j.jprot.2017.10.011

Bucio-Noble, D., Kautto, L., Krisp, C., Ball, M.S., Molloy, M.P.Polyphenol extracts from dried sugarcane inhibit inflammatory mediators in an in vitro colon cancer model Journal of Proteomics 10.1016/j.jprot.2018.02.009

Ashwood, C., Lin, C.-H., Thaysen-Andersen, M., Packer, N.H.Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS Journal of the American Society for Mass Spectrometry 10.1007/s13361-018-1932-z

Varela, C., Schmidt, S.A., Borneman, A.R., Pang, C.N.I., Krömerx, J.O., Khan, A., Song, X., Hodson, M.P., Solomon, M., Mayr, C.M., Hines, W., Pretorius, I.S., Baker, M.S., Roessner, U., Mercurio, M., Henschke, P.A., Wilkins, M.R., Chambers, P.J.Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains Metabolic Engineering 10.1016/j.ymben.2018.08.006

Fathi, A., Mirzaei, M., Dolatyar, B., Sharifitabar, M., Bayat, M., Shahbazi, E., Lee, J., Javan, M., Zhang, S.-C., Gupta, V., Lee, B., Haynes, P.A., Baharvand, H., Salekdeh, G.H.Discovery of novel cell surface markers for purification of embryonic dopamine progenitors for transplantation in Parkinson’s disease animal models Molecular and Cellular Proteomics 10.1074/mcp.RA118.000809

Edouard C Nice, Liyuan Peng, David I Cantor, Canhua Huang, Kui Wang, Mark S BakerTissue and plasma proteomics for early stage cancer detection .Molecular Omics 10.1039/c8mo00126j

Patel, S., Masi, A., Dale, R.C., Whitehouse, A.J.O., Pokorski, I., Alvares, G.A., Hickie, I.B., Breen, E., Guastella, A.J.Social impairments in autism spectrum disorder are related to maternal immune history profile Molecular Psychiatry 10.1038/mp.2017.201

Bezawork-Geleta, A., Wen, H., Dong, L., Yan, B., Vider, J., Boukalova, S., Krobova, L., Vanova, K., Zobalova, R., Sobol, M., Hozak, P., Novais, S.M., Caisova, V., Abaffy, P., Naraine, R., Pang, Y., Zaw, T., Zhang, P., Sindelka, R., Kubista, M., Zuryn, S., Molloy, M.P., Berridge, M.V., Pacak, K., Rohlena, J., Park, S., Neuzil, J.Alternative assembly of respiratory complex II connects energy stress to metabolic checkpoints Nature Communications 10.1038/s41467-018-04603-z

Ghazizadeh, Z., Fattahi, F., Mirzaei, M., Bayersaikhan, D., Lee, J., Chae, S., Hwang, D., Byun, K., Tabar, M.S., Taleahmad, S., Mirshahvaladi, S., Shabani, P., Fonoudi, H., Haynes, P.A., Baharvand, H., Aghdami, N., Evans, T., Lee, B., Salekdeh, G.H.Prospective Isolation of ISL1+Cardiac Progenitors from Human ESCs for Myocardial Infarction Therapy Stem Cell Reports 10.1016/j.stemcr.2018.01.037

Ghaffari, M.R., Mirzaei, M., Ghabooli, M., Khatabi, B., Wu, Y., Zabet-Moghaddam, M., Mohammadi-Nejad, G., Haynes, P.A., Hajirezaei, M.R., Sepehri, M. and Salekdeh, G.HRoot endophytic fungus Piriformospora indica improves drought stress adaptation in barley by metabolic and proteomic reprogramming Environmental and Experimental Botany doi.org/10.1016/j.envexpbot.2018.10.002

Chitranshi, N., Dheer, Y., Mirzaei, M., Wu, Y., Salekdeh, G.H., Abbasi, M., Gupta, V., Vander Wall, R., You, Y., Graham, S.L. and Gupta, VLoss of Shp2 Rescues BDNF/TrkB Signalling and Contributes to Improved Retinal Ganglion Cells Neuroprotection Molecular Therapy doi.org/10.1016/j.ymthe.2018.09.019

Shen T., You Y., Joseph C., Mirzaei M., Klistorner A., Graham S.L., Gupta V.BDNF Polymorphism: A Review of Its Diagnostic and Clinical Relevance in Neurodegenerative Disorders Aging and Disease doi:  10.14336/AD.2017.0717

Amjadi F., Mehdizadeh M., Ashrafi M., Nasrabadi D., Taleahmad S., Mirzaei M., Gupta V., Salekdeh G.H., Aflatoonian R.Distinct changes in the proteome profile of endometrial tissues in polycystic ovary syndrome compared with healthy fertile women Reproductive biomedicine online doi.org/10.1016/j.rbmo.2018.04.043

Dheer Y., Chitranshi N., Gupta V., Abbasi M., Mirzaei M., You Y., Chung R., Graham S.L., Gupta V.Bexarotene Modulates Retinoid-X-Receptor Expression and Is Protective Against Neurotoxic Endoplasmic Reticulum Stress Response and Apoptotic Pathway Activation Molecular neurobiology doi.org/10.1007/s12035-018-1041-9

Emery, S.J., Baker, L., Ansell, B.R., Mirzaei, M., Haynes, P.A., McConville, M.J., Svärd, S.G. and Jex, A.R.Differential protein expression and post-translational modifications in Metronidazole-resistant Giardia duodenalis GigaScience doi.org/10.1093/gigascience/giy024


Su Yin Lim, Jenny H. Lee, Sarah J. Welsh, Seong Beom Ahn, Edmond Breen, Alamgir Khan, Matteo S. Carlino, Alexander M. Menzies, Richard F. Kefford, Richard A. Scolyer, Georgina V. Long and Helen Rizos. Evaluation of two high-throughput proteomic technologies for plasma biomarker discovery in immunotherapy treated melanoma patients. Biomarker Research (2017) 5:32 DOI 10.1186/s40364-017-0112-9

Wu JX, Pascovici D, Ignjatovic V, Song X, Krisp C, Molloy MP. Improving Protein Detection Confidence Using SWATH-Mass Spectrometry with Large Peptide Reference Libraries. Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700174.

Lee A, Rayner SL, De Luca A, Gwee SSL, Morsch M, Sundaramoorthy V, Shahheydari H, Ragagnin A, Shi B, Yang S, Williams KL, Don EK, Walker AK, Zhang KY, Yerbury JJ, Cole NJ, Atkin JD, Blair IP,Molloy MP, Chung RS. Casein kinase II phosphorylation of cyclin F at serine 621 regulates the Lys48-ubiquitylation E3 ligase activity of the SCF((cyclin F)) complex. Open Biol. 2017 Oct;7(10). pii:170058. doi: 10.1098/rsob.170058.

Mirzaei M, Gupta VB, Chick JM, Greco TM, Wu Y, Chitranshi N, Wall RV, Hone E, Deng L, Dheer Y, Abbasi M, Rezaeian M, Braidy N, You Y, Salekdeh GH, Haynes PA, Molloy MP, Martins R, Cristea IM, Gygi SP, Graham SL, Gupta VK. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Sci Rep. 2017 Oct 4;7(1):12685. doi:10.1038/s41598-017-12858-7.

Kamath KS, Krisp C, Chick J, Pascovici D, Gygi SP, Molloy MP. Pseudomonas aeruginosa Proteome under Hypoxic Stress Conditions Mimicking the Cystic Fibrosis Lung. J Proteome Res. 2017 16(10), 3917-3928.

Tan S-H, Lee A, Pascovici D, Care N, Birzniece V, Ho K, Molloy MP, Khan A. Plasma biomarker proteins for detection of human growth hormone administration in athletes. Scientific Reports 7, 10039., doi:10.1038/s41598-017-09968-7.

Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras A-C, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng S-C, Zhang H, Aebersold R.  Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat. Commun. 2017 doi: https://doi.org/10.1101/074567

Ahuja R, Almuzian M, Khan A, Pascovici D, Dalci O, Darendeliler M. A preliminary investigation of short-term cytokine expression in gingival crevicular fluid secondary to high-level orthodontic forces and the associated root resorption: case series analytical study. Progress in orthodontics 2017; 18: 23.

Breen EJ. Protein Multiplexed Immunoassay Analysis with R. Methods Mol Biol. 2017;1619:495-537. doi: 10.1007/978-1-4939-7057-5_35.

O’Doherty PJ, Khan A, Johnson AJ, Rogers PJ, Bailey TD, Wu MJ. Proteomic response to linoleic acid hydroperoxide in Saccharomyces cerevisiae.FEMS Yeast Research, 17, 2017, fox022, doi: 10.1093/demsyr/fox022

Krisp C, Molloy MP. SWATH Mass Spectrometry for Proteomics of Non-Depleted Plasma. Methods Mol Biol. 2017;1619:373-383. doi: 10.1007/978-1-4939-7057-5_25. PubMed PMID: 28674897

McRobb LS, McKay MJ, Gamble JR, Grace M, Moutrie V, Santos ED, Lee VS, Zhao Z, Molloy MP, Stoodley MA. Ionizing radiation reduces ADAM10 expression in brain microvascular endothelial cells undergoing stress-induced senescence. Aging (Albany NY). 2017 Apr 17. doi: 10.18632/aging.101225.

Hogan AL, Don EK, Rayner SL, Lee A, Laird AS, Watchon M, Winnick C, Tarr IS, Morsch M, Fifita JA, Gwee S, Formella I, Hortle E, Yuan K, Molloy MP, Williams KL, Nicholson GA, Chung RS, Blair IP, Cole NJ. Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype. Hum Mol Genet. 2017 Apr 21. doi: 10.1093/hmg/ddx136. [Epub ahead of print] PubMed PMID: 28444311.

Bjelosevic S, Pascovici D, Ping H, Karlaftis V, Zaw T, Song X, Molloy MP, Monagle P, Ignjatovic V. Quantitative age-specific variability of plasma proteins in healthy neonates, children and adults. Mol Cell Proteomics. 2017 Mar 23. pii: mcp.M116.066720. doi: 10.1074/mcp.M116.066720.

Everest-Dass AV, Kolarich D, Pascovici D, Packer NH. Blood group antigen expression is involved in C. albicans interaction with buccal epithelial cells. Glycoconj J. 2017 Feb;34(1):31-50.

Simonian M, Loo RRO, Rannulu N, Loo JA, Molloy MP, Stoodley MA.  Identification of protein targets in cerebral endothelial cells for brain arteriovenous malformation (AVMs) molecular therapies. Clin Proteom (2017) 14:17.

Mirzaei M, Pascovici D, Wu JX, Chick J, Wu Y, Cooke B, Haynes P, Molloy MP. TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform. Methods Mol. Biol. 2017;1549:45-66.

Johnson AJ, Zaman MS, Veljanoski F, Phrakaysone A, Li S, O’Doherty PJ, Petersingham G, Perrone GG, Molloy MP and Wu MJ. Unravelling the role of protein kinase CK2 in metal toxicity by gene deletion mutants. Metallomics, 2017 Feb 14. doi: 10.1039/c6mt00230g. [Epub ahead of print].

McRobb LS, Lee VS, Simonian M, Zhao Z, Thomas SG, Wiedmann M, Raj JV, Grace M, Moutrie V, McKay MJ, Molloy MP, Stoodley MA. Radiosurgery Alters the Endothelial Surface Proteome: Externalized Intracellular Molecules as Potential Vascular Targets in Irradiated Brain Arteriovenous Malformations. Radiat. Res. 2017 Jan; 187(1):66-78

Truong HH, Neilson KA, McInerney BV, Khoddami A, Roberts TH, Cadogan DJ, Liu SY, Selle PH. Comparative performance of broiler chickens offered nutritionally equivalent diets based on six diverse,‘tannin-free’sorghum varieties with quantified concentrations of phenolic compounds, kafirin, and phytate. Animal Production Science 2017; 57: 828-838.

Yashin D, Dalci O, Almuzian M, Chiu J, Ahuja R, Goel A, Darendeliler M. Markers in blood and saliva for prediction of orthodontically induced inflammatory root resorption: a retrospective case controlled-study. Progress in orthodontics 2017; 18: 27.


Breen EJ. Sample Replication Effects on Statistical Power in Multiplexed Immunoassay Analysis. MOJ Proteomics Bioinform 2016, 4(3): 00121.

Selle PH, Truong HH, McQuade LR, Moss AF, Liu SY. Reducing agent and exogenous protease additions, individually and in combination, to wheat- and sorghum-based diets interactively influence parameters of nutrient utilisation and digestive dynamics in broiler chickens. Animal Nutrition, Volume 2, Issue 4, December 2016, Pages 303-311.

Morris KM, O'Meally D, Zaw T, Song X, Gillett A, Molloy MP, Polkinghorne A, Belov K. Characterisation of the immune compounds in koala milk using a combined transcriptomic and proteomic approach. Sci Rep. 2016 Oct 7;6:35011.

Pascovici D, Handler DC, Wu JX, Haynes PA. Multiple testing corrections in quantitative proteomics: A useful but blunt tool. Proteomics. 2016 Sep;16(18):2448-53.

Al-Eisawi Z, Beale P, Chan C, Yu JQ, Proschogo N, Molloy M, Huq F. .Changes in the in vitro activity of platinum drugs when administered in two aliquots. BMC Cancer. 2016 Aug 26; 16:688.

Mirzaei M, Wu Y, Handler D, Maher T, Pascovici D, Ravishankar P. (Ed.) in Applications of Quantitative Proteomics in Plant Research, Agricultural Proteomics Volume 1, 1-29, Springer International Publishing.

Mahboob S, Ahn SB, Mohamedali A, Amirkhani A, Tan S-H, Ranganathan S, Nice E and Baker MS. Addition of protease inhibitors to EDTA containing blood collection tubes does not deliver significant advantage for preservation of plasma for down-stream analysis. Clin Proteom Bioinform, 2016, Volume 1(3): 1-9.

Song X, Amirkhani A, Wu JX, Pascovici D, Zaw T, Xavier D, Clarke SJ, Molloy MP. Analytical performance of nanoLC-SRM using non-depleted human plasma over an 18-month period. Proteomics.2016 Aug;16(15-16):2118-27

Wu JX, Song X, Pascovici D, Zaw T, Care N, Krisp C, Molloy MP. SWATH mass spectrometry performance using extended peptide MS/MS assay libraries. Mol. Cell. Proteomics. 2016 Jul;15(7):2501-14.

Hayes SA, Haefliger S, Harris B, Pavlakis N, Clarke SJ, Molloy MP, Howell VM. Exhaled breath condensate for lung cancer protein analysis: a review of methods and biomarkers. J. Breath Res. 2016 Jul 5;10(3):034001.

Kamath KS, Pascovici D, Penesyan A, Goel A, Venkatakrishnan V, Paulsen IT, Packer NH, Molloy MP. Pseudomonas aeruginosa cell membrane protein expression from phenotypically diverse cystic fibrosis isolates demonstrate host specific adaptations. J Proteome Res. 2016 Jul 1;15(7):2152-63.

Wu Y, Mirzaei M, Pascovici D, Chick JM, Atwell BJ, Haynes PA. Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease. J Proteomics. 2016 Jun 30;143:73-82.

Truong HH, Neilson KA, McInerney BV, Khoddami A, Roberts TH, Cadogan DJ, Liu SY and Selle PH. Comparative performance of broiler chickens offered nutritionally equivalent diets based on six diverse, ‘tanninfree’ sorghum varieties with quantified concentrations of phenolic compounds, kafirin, and phytate. Animal Production Science http://dx.doi.org/10.1071/AN16073. Submitted: 8 February 2016 Accepted: 9 February 2016 Published online: 1 June 2016

Breen EJ Tan W, and Khan A. The Statistical Value of Raw Fluorescence Signal in Luminex xMAP Based Multiplex Immunoassays. Scientific Reports, 2016 May 31;6:26996.

Williams KL, Topp S, Yang S, Smith B, Fifita JA, Warraich ST, Zhang KY, Farrawell N, Vance C, Hu X, Chesi A, Leblond CS, Lee A, Rayner SL, Sundaramoorthy V, Dobson-Stone C, Molloy MP, Van Blitterswijk M, Dickson DW, Petersen RC, Graff-Radford NR, Boeve BF, Murray ME, Pottier C, Don E, Winnick C, McCann EP, Hogan A, Daoud H, Levert A, Dion PA, Mitsui J, Ishiura H, Takahashi Y, Goto J, Kost J, Gellera C, Gkazi AS, Miller J, Stockton J, Brooks WS, Boundy K, Polak M, Muñoz-Blanco JL, Esteban-Pérez J, Rábano A, Hardiman O, Morrison KE, Ticozzi N, Silani V, De Belleroche J, Glass JD, Kwok JBJ, Guillemin GJ, Chung RS, Tsuji S, Brown RH Jr, García-Redondo A, Rademakers R, Landers JE, Gitler AD, Rouleau GA, Cole NJ, Yerbury JJ, Atkin JD, Shaw CE, Nicholson GA, Blair IP. CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia. Nat Comm, Volume 7, 15 April 2016, Article number 11253.

Liu C, Song X, Nisbet R, and Götz J. Co-immunoprecipitation with tau isoform-specific antibodies reveals distinct protein interactions, and highlights a putative role for 2N tau in disease. The Journal of Biological Chemistry. 2016 Apr 8;291(15):8173-88

Martinez-Aguilar J, Clifton-Bligh R, Molloy MP. Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy. Scientific Reports, 2016 Mar 30;6:23660.

Kao SC, Kirschner, MB, Cooper, WA, Tran T, Burgers S, Wright C, Korse T, van den Broek D, Edelman J, Vallely M, McCaughan B, Pavlakis N, Clarke S, Molloy MP, van Zandwijk N, Reid G. A proteomics-based approach identifies secreted protein acidic and rich in cysteine (SPARC) as a prognostic biomarker in malignant pleural mesothelioma. Br. J. Cancer 2016, Mar 1;114(5):524-31.

Eaton TR, Potter A, Billaut F, Panchuk D, Pyne DB, Gore CJ, Chen TT, McQuade L, Stepto NK. A Combination of Amino Acids and Caffeine Enhances Sprint Running Capacity in a Hot, Hypoxic Environment. Int J Sport Nutr Exerc Metab. 2016 Feb;26(1):33-45.

Succar P, Medynskyj M, Breen EJ, Batterham T, Molloy MP and Herbert BR. Priming Adipose-Derived Mesenchymal Stem Cells with Hyaluronan Alters Growth Kinetics and Increases Attachment to Articular Cartilage. Stem Cells International Volume 2016, Article ID 9364213, 13 pages

D’Agostino PMD, Song X, Neilan BA, Moffitt MC. Proteogenomics of a saxitoxin-producing and non-toxic strain of Anabaena circinalis (cyanobacteria) in response to extracellular NaCl and phosphate depletion. Environ Microbiol. 2016 Feb;18(2):461-76.

Jamieson C, Mills KM, Lui C, Semaan C, Molloy MP, Sharma M, Forwood JK, Henderson BR. Characterization of a beta-catenin nuclear localization defect in MCF-7 breast cancer cells. Exp Cell Res.2016 Feb 15;341(2):196-206.

Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA. Induction of virulence factors in Giardia duodenalis independent of host attachment. Sci Rep. 2016 Feb 12;6:20765.

Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res. 2016 Feb 5;15(2):339-59.


Kaufman K, Jenkins Y, Alomari M, Mirzaei M, Best O, Pascovici D, Mactier S, Mulligan S, Haynes P, Christopherson RI. The Hsp90 inhibitor SNX-7081 is synergistic with fludarabine nucleoside via DNA damage and repair mechanisms in human, p53-negative chronic lymphocytic leukemia. Oncotarget. 2015 Dec 1;6(38):40981-97.

Jankova L, Dent OF, Molloy MP, Chan C, Chapuis PH, Howell VM, Clarke SJ. Reporting in studies of protein biomarkers of prognosis in colorectal cancer in relation to the REMARK guidelines. Proteomics Clin Appl. 2015 Dec;9(11-12):1078-86

Huang PY, Mactier S, Armacki N, Giles Best O, Belov L, Kaufman KL, Pascovici D, Mulligan SP, Christopherson RI. Protein profiles distinguish stable and progressive chronic lymphocytic leukemia. Leuk Lymphoma. 2015 Nov 16:1-11.

Meex RC, Hoy AJ, Morris A, Brown RD, Lo JC, Burke M, Goode RJ, Kingwell BA, Kraakman MJ, Febbraio MA, Greve JW, Rensen SS, Molloy MP, Lancaster GI, Bruce CR, Watt MJ. Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism. Cell Metab. 2015 Oct 20. pii: S1550-4131(15)00480-5.

Penesyan A, Kumar SS, Kamath K, Shathili AM, Venkatakrishnan V, Krisp C, Packer NH, Molloy MP, Paulsen IT. Genetically and phenotypically distinct Pseudomonas aeruginosa cystic fibrosis isolates share a core proteomic signature. PLOS One 2015 Oct 2;10(10):e0138527

Schilter H, Cantemir-Stone CZ, Leksa V, Ohradanova-Repic A, Findlay AD, Deodhar M, Stockinger H, Song X, Molloy M, Marsh CB, Jarolimek W. The mannose-6-phosphate analogue, PXS64, inhibits fibrosis via TGF-β1 pathway in human lung fibroblasts. Immunol Letters 2015, 165(2), 90-101.

Su SP, Song X, Xavier D, Aquilina JA. Age-related cleavages of crystallins in human lens cortical fiber cells generate a plethora of endogenous peptides and high molecular weight complexes. Proteins. 2015 Oct;83(10):1878-86.

Sowmya G, Breen EJ, Ranganathan S. Linking structural features of protein complexes and biological function. Protein Sci, 2015 Sep;24(9):1486-94

George I S, Pascovici D, Mirzaei M, Haynes PA. Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism. Proteomics. 2015 Sep;15(17):3048-60

Trewin AJ, Lundell LS, Perry BD, Patil KV, Chibalin AV, Levinger I, McQuade LR, Stepto NK. Effect of N-acetylcysteine infusion on exercise-induced modulation of insulin sensitivity and signaling pathways in human skeletal muscle. Am J Physiol Endocrinol Metab. 2015 Aug 15;309(4):E388-97

Liu SY, Fox G, Khoddami A, Neilson KA, Truong HH, Moss AF and Selle PH, Grain Sorghum: A Conundrum for Chicken-Meat Production Agriculture 2015, 5, 1224-1251;

Truong HH, Neilson KA, McInerney BV, Khoddami A, Roberts TH, Liu SY, Selle PH. Performance of broiler chickens offered nutritionally-equivalent diets based on two red grain sorghums with quantified kafirin concentrations as intact pellets or re-ground mash following steam-pelleting at 65 or 97°C conditioning temperatures Animal Nutrition1(2015)220–228

Percy AJ, Tamura-Wells J, Albar JP, Aloria K, Amirkhani A, Araujo GDT, Arizmendi JM, Blanco FJ, Canals F, Cho J-Y, Colomé-Calls N, Corrales FJ, Domont G, Espadas G, Fernandez-Puente P, Gil C, Haynes PA, Hernáez ML, Kim JY, Kopylov A, Marcilla M, McKay MJ, Mirzaei M, Molloy MP, Ohlund LB, Paik Y-K, Paradela A, Raftery M, Sabidó E, Sleno L, Wilffert D, Wolters JC, Yoo JS, Zgoda V, Parker CE, Borchers CH. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accurancy and reproducibility assessment. EuPA Open Proteomics. 2015, Vol.8, p.6-15

Mahon, K., Lin, H-M., Castillo, L., Lee, B., Lee-Ng, M., Chatfield, M., Chiam, K., Breit,S., Brown, D., Marx, G., Molloy, MP, Pavlakis, N., Boyer, M., Stockler, MR., Daly, R.J., Henshall, S., Horvath, L. Cytokine profiling of docetaxel-resistant castration resistant prostate cancer. Br. J. Cancer 2015, 112, 1340–1348.

Herbert B R, Succar P, Breen E J and Kuah D E K. Alterations in the Secretome of Clinically Relevant Preparations of Adipose-Derived Mesenchymal Stem Cells Co-Cultured with Hyaluronan. Stem Cells International, 2015:2015:421253

Krisp C, Yang H, van Soest R, Molloy MP. Online peptide fractionation using a multiphasic microfluidic LC chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics. Mol Cell Proteomics. 2015 Jun;14(6):1708-19

Emery S J, Pascovici D, Lacey E, Haynes P A. The generation gap: Proteome changes and strain variation during encystation in Giardia duodenalis. Mol Biochem Parasitol. 2015 May; 201(1):47-56

Parker R, Vella L, Xavier D, Amirkhani A, Parker J, Cebon J, Molloy M. Phosphoproteomic analysis of cell-based resistance to BRAF inhibitor therapy in melanoma. Front. Oncol. 2015, May 15;5:95.

Mahboob S, Ahn SB, Cheruku HR, Cantor D, Rennel E, Fredriksson S, Edfeldt G, Breen EJ, Khan A, Mohamedali A, Muktadir MG, Ranganathan S, Tan S-H, Nice E and Baker MS. A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes’ stages A-D colorectal cancers. Clinical Proteomics 2015, April 8;12(1):10.

Martinez-Aguilar J, Clifton-Bligh R, Molloy MP. A multiplexed, targeted mass spectrometry assay of the S100 protein family uncovers the isoform-specific expression in thyroid tumours. BMC Cancer 2015 Mar 29;15:199.

Fernando, N; Panozzo, J; Tausz, M; Norton, R; Fitzgerald, G; Khan, A, Seneweera, S. S. Rising CO2 concentration altered wheat grain proteome and flour rheological characteristics. Food Chem 2015,1;70: 448-454

Breen, E J; Polaskova, V; Khan, A. Bead-based multiplex immune-assays for cytokines, chemokines, growth factors and other analytes: Median fluorescence intensities versus their derived absolute concentration values for statistical analysis. Cytokine 2015 Feb;71(2):188-198.

Kamath, K S; Kumar, S S; Kaur, J; Venkatakrishnan, V; Paulsen, I T; Nevalainen, H; Molloy, M P. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl. 2015 Feb;9(1-2):134-46.
Pascovici D, Song X, Solomon P S, Winterberg B Mirzaei M, Goodchild A, Stanley W C, Liu J and Molloy M P. Combining Protein Ratio p-Values as a Pragmatic Approach to the Analysis of Multirun iTRAQ Experiments. J Proteome Res. 2015, Feb 6;14(2), 738-746.Lin C-H, Chik J H L, Packer N H, Molloy M P. Multidimensional Fractionation is a Requirement for Quantitation of Golgi-Resident Glycosylation Enzymes from Cultured Human Cells. J Proteome Res, 2015, Feb 6;14(2):747-55


McQuade LR, Balachandran A, Scott HA, Khaira S, Baker MS, Schmidt U. Proteomics of Huntington's disease-affected human embryonic stem cells reveals an evolving pathology involving mitochondrial dysfunction and metabolic disturbances. J Proteome Res. 2014 Dec 5;13(12):5648-59.

Krisp, C; Hebert, N; McKay, M; Yang, M; Van Soest, R; Settineri, T; Molloy, M P. MudCHiP: Online 2D chip-LC Peptide Trapping as a Robust Approach for Proteomic Biomarker Applications. J. Biomol. Tech. 2014;25(Suppl):S24-S25.

Kaufman, K L; Ly, L; McKay, M; Mallawaarachty, D M; Mactier, S; Crossett, B; Molloy, M; Buckland, M E; McDonald, K L and Christopherson, R I. Comprehensive proteomic profiling of bevacizumab-resistant glioblastoma. NeuroOncology 2014, 16(Suppl 2) ii98.

Liang, V I; Ullrich, M; Lam, H; Chew, Y L; Banister, S; Song, X; Zaw, T; Kassiou, M; Götz, J; Nicholas, H R. Altered proteostasis in aging and heat shock response in C. elegans revealed by analysis of the global and de novo synthesized proteome. Cell Mol Life Sci. 2014 Sep;71(17):3339-61.

Huang, P Y; Best, O G; Almazi, J G; Belov, L; Davis, Z A; Majid, A; Dyer, M J; Pascovici, D; Mulligan, S P; Christopherson, R I. Cell surface phenotype profiles distinguish stable and progressive chronic lymphocytic leukemia. Leuk Lymphoma. 2014 Sep;55(9):2085-92

Rogers, L J; Suchowerska, N; Khan, A; Polaskova, V; McKenzie, D R. Profiling of the secretome of human cancer cells: Preparation of supernatant for proteomic analysis. Electrophoresis. 2014 Sep;35(18):2626-33.

Ullrich M, Liang V, Chew YL, Banister S, Song X, Zaw T, Lam H, Berber S, Kassiou M, Nicholas HR, Götz J. Bio-orthogonal labeling as a tool to visualize and identify newly synthesized proteins in Caenorhabditis elegans. Nat Protoc. 2014 Sep;9(9):2237-2255.

Ahn, S-B; Khan, A. Detection and quantitation of twenty-seven cytokines, chemokines and growth factors pre- and post-high abundance protein depletion in human plasma. EuPA Open Proteomics 3 (2014) 78-84.

Chik, J H; Zhou, J; Moh, E S; Christopherson, R; Clarke, S J; Molloy, M P; Packer, N H. Comprehensive glycomics comparison between colon cancer cell cultures and tumours: Implications for biomarker studies. J Proteomics. 2014 Aug 28; 108:146-62.

Winterberg B, Du Fall LA, Song X, Pascovici D, Care N, Molloy M, Ohms S, Solomon PS. The necrotrophic effector protein SnTox3 re-programs metabolism and elicits a strong defence response in susceptible wheat leaves. BMC Plant Biol. 2014 Aug 15;14(1):215.

Vörös, A; Simm, R; Slamti, L; McKay, M J; Hegna, I K; Nielsen-LeRoux, C; Hassan, K A; Paulsen, I T; Lereclus, D; Okstad, O A; Molloy, M P; Kolstø, A B. SecDF as Part of the Sec-Translocase Facilitates Efficient Secretion of Bacillus cereus Toxins and Cell Wall-Associated Proteins. PLoS One. 2014 Aug 1;9(8):e103326.

Parker, R; Clifton-Bligh, R; Molloy, M P. Phosphoproteomics of MAPK inhibition in BRAF mutated cells and a role for the lethal synergism of dual BRAF and CK2 inhibition. Mol Cancer Ther. 2014 Jul; 13(7): 1894-906.

Simonian M, Ogorzalek Loo RR, Loo JA, Stoodley MA, Molloy MP. “Proteomics Detection of Endothelial Cell Surface Proteins Following Irradiation as Potential Targets for Brain Arteriovenous Malformations Molecular Therapy.” MOJ Proteomics Bioinform 2014; 1: 00002 (6 pp.).

Hayes, S A; Hudson, A L; Clarke, S J; Molloy, M P; Howell, V M. From mice to men: GEMMs as trial patients for new NSCLC therapies. Semin Cell Dev Biol. 2014 Mar; 27:118-27.

Hart-Smith, G; Chia, S Z; Low, J K; McKay, M J; Molloy, M P; Wilkins, M R. Stoichiometry of Saccharomyces cerevisiae lysine methylation: insights into non-histone protein lysine methyltransferase activity. J Proteome Res. 2014 Mar 7; 13(3):1744-56.

D’Agostino, P M; Song, X; Neilan, B A; Moffitt, M C. Comparative proteomics reveals that a saxitoxin-producing and a nontoxic strain of Anabaena circinalis are two different ecotypes.  J. Proteome Res. 2014 Mar 7; 13(3): 1474-84.

Brinkman, D L; Konstantakopoulos, N; McInerney, B V; Mulvenna, J; Seymour, J E; Isbister, G K; Hodgson, W C. Chironex fleckeri (box jellyfish) venom proteins: expansion of a cnidarian toxin family that elicits variable cytolytic and cardiovascular effects. J. Biol.Chem. 2014 Feb 21; 289(8):4798-812.

Mirzaei, M; Soltani, N; Sarhadi, E; George, I S; Neilson, K A; Pascovici, D; Shahbazian, S; Haynes, P A; Atwell, B J; Salekdeh, G H. Manipulating root water supply elicits major shifts in the shoot proteome. J Proteome Res. 2014 Feb 7; 13(2):517-26.


Trewin, A J; Petersen, A C; Billaut, F; McQuade, L R; McInerney, B V; Stepto, N K. N-acetylcysteine alters substrate metabolism during high-intensity cycle exercise in well-trained humans. Appl. Physiol. Nutr. Metab. 2013 Dec; 38(12): 1217-27.

Ghabooli, M; Khatabi, B; Ahmadi, F S; Sepehri, M; Mirzaei, M; Amirkhani, A; Jorrin-Novo, J V; Salekdeh, G H. Proteomics study reveals the molecular mechanisms underlying water stress tolerance induced by Piriformospora indica in barley. J Proteomics 2013 Dec 6; 94:289-301.

Pascovici, D; Gardiner, D M; Song, X; Breen, E; Solomon, P S; Keighley, T; Molloy, M P. Coverage and consistency: Bioinformatics aspects of the analysis of multi-run iTRAQ experiments with wheat leaves. J Proteome Res. 2013 Nov 1; 12(11):4870-81.

Krisp, C; Jacobsen, F; Steinstraesser, L; McKay, M J; Molloy, M P; Wolters, D A. Proteome analysis reveals anti-angiogenic environments in chronic wounds of diabetes mellitus Type 2 patients. Proteomics. 2013 Sep; 13(17): 2670-81.

Martinez-Aguilar, J and Molloy, M P. Label-free selected reaction monitoring enables multiplexed quantitation of S100 protein isoforms in cancer cells. J. Proteome Res. 2013 Aug 2; 12(8):3679-88.

Wongtrakul-Kish, K; Kolarich, D; Pascovici, D; Joss, J L; Deane, E; Packer, N H. Characterization of N- and O-linked glycosylation changes in milk of the tammar wallaby (Macropus eugenii) over lactation. Glycoconj. J. 2013 Jul;30(5):523-36.

Cantor, D; Slapetova, I; Kan, A; McQuade, L R; Baker, M S. Overexpression of αvβ6 integrin alters the colorectal cancer cell proteome in favor of elevated proliferation and a switching in cellular adhesion that increases invasion. J Proteome Res. 2013 Jun 7; 12(6):2477-90.

Neilson, K A; Keighley, T; Pascovici, D; Cooke, B; Haynes, P A. Label-free quantitative shotgun proteomics using normalized spectral abundance factors. Methods Mol Biol. 2013, 1002:205-22.

Lee, A; Molloy, M P; Baker, M S; Kapur, A. Tandem ion exchange fractionation of chicken egg white reveals the presence of proliferative bioactivity. J. Agric. Food Chem. 2013 May 1; 61(17): 4079-88.

Molloy, M P. Two-stepping to increase peptide spectra matches in large databases. Proteomics 2013 Apr; 13(8): 1229-30.

Cramer, G R; Van Sluyter, S C; Hopper, D W; Pascovici, D; Keighley, T; Haynes, P A. Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit. BMC Plant Biol. 2013 Mar 21;13:49

Monavarfeshani, A; Sarhadi, E; Amirkhani, A; Haynes, P A; Nekouei, M K; Mardi, M; Mirzaei, M; Salekdeh, G H. Shotgun proteomic analysis of the Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia". J. Proteome Res. 2013 Feb 1;12(2):785-95.

Boeuf, P; Aitken,E H; Chandrasiri, U; Chua, C L L; McInerney, B; McQuade, L; Duffy, M; Molyneux, M; Brown, G; Glazier, J; Rogerson, S J. Plasmodium falciparum malaria elicits inflammatory responses that dysregulate placental amino acid transport. PLoS Pathog 2013 Feb; 9(2): e1003153.

Kumar, G; Breen, E J; Ranganathan, S. Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. BMC Systems Biology 2013 Feb 6; 7:12

Martínez-Aguilar, J; Chik, J; Nicholson, J; Semaan, C; McKay, M J; Molloy, M P. Quantitative mass spectrometry for colorectal cancer proteomics. Proteomics Clin Appl. 2013 Jan;7(1-2):42-54.


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.


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.


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.


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.

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.


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.

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