Publications & Expertise

Dr. Mirzaei’s new book, Modern Proteomics – Sample Preparation, Analysis and Practical Applications (Advances in Experimental Medicine and Biology), has been published! Click here to order.

The staff of the proteomics core collaborate closely with customers, and are often heavily involved in the write-up process of projects that have made use of mass spectrometry services. If you are a customer of the core, and have published work that made use of the proteomics services that we offer, we’d like to list your publication here. Please contact us with details.

Selected Customer & Collaborator Publications

Kalantari, R., Hicks, J.A., Li, L., Gagnon, K.T., Sridhara, V., Lemoff, A., Mirzaei, H., Corey, D.R. (2016). Stable Association of RNAi Machinery is Conserved Between the Cytoplasm and Nucleus of Human Cells, RNA, 22, 1085-1098.

Theodoropoulos, P., Gonzalez, S.S., Winterton, S.E., Rodriguez-Navas, C., McKnight, J.S., Morlock, L., Hanson, J., Cross, B., Owen, A.E., Duan, Y., Moreno, J.R., Lemoff, A., Mirzaei, H., Posner, B.A., Williams, N.S., Ready, J.M., Nijhawan, D. (2016) Discovery of Tumor-Specific Irreversible Inhibitors of Stearoyl CoA Desaturase, Nature Chemical Biology, 12, 218-225.

Wands, A.M., Fujita, A., McCombs, J.E., Nygren, J., Rodriguez, A.C., Nischan, N., Bond, M.R., Mettlen, M., Reis, C.R. Trudgian, D.C., Lemoff, A., Steentoft, C., Clausen, H., Schmid, S.L., Mirzaei, H., Yrlid, U., Kohler, J.J., Fucosylation and protein glycosylation create functional receptors for cholera toxin, eLife, 4, e09545.

Yamashiro, Y., Papke, C. L., Kim, J., Ringuette, L. J., Zhang, Q. J., Liu, Z. P., Mirzaei, H., Wagenseil, J. E.. Davis, E. C., Yanagisawa, H. (2015). Abnormal mechanosensing and cofilin activation promotes the progression of ascending aortic aneurysms in mice, Science Signaling, 8.

Salomon, D., Klimko, J. A., Trudgian, D. C., Kinch, L. N., Grishin, N. V., Mirzaei, H., Orth, K. (2015). Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria, Plos Pathogens, 11 (8).

Katafuchi, T., Esterházy, D., Lemoff, A., Ding, X., Kliewer, S.A., Mirzaei, H., Mangelsdorf, D.J. (2015). Detection of FGF15 in Plasma by Stable Isotope Standards and Capture by Anti-Peptide
Antibodies (SISCAPA) and Targeted Mass Spectrometry, Cell Metabolism, 2015, 21, 898-904.

Wang, G., Han, T., Nijhawan, D., Theodoropoulos, P., Naidoo, J., Yadavalli, S., Mirzaei, H., Pieper, A. A., Ready, J. M., McKnight, S. L. (2014). P7C3 Neuroprotective Chemicals Function by Activating the Rate-Limiting Enzyme in NAD Salvage, Cell, 158 (6), 1324-1334.

Salomon, D., Kinch, L. N., Trudgian, D. C., Guo, X. F., Klimko, J. A., Grishin, N. V., Mirzaei, H., Orth, K. (2014), Marker for type VI secretion system effectors, PNAS, 111 (25), 9271-9276.

Yamashiro, Y., Huang, J. B., Papke, C. L., Mirzaei, H., Yanagisawa, H. (2013). Identification of Key Modulators Involved in Aortic Aneurysm Formation In Fibulin-4 Deficient Mice, Circulation, 128 (22).

Sengupta, S., Lorente-Rodriguez, A., Earnest, S., Stippec, S., Guo, X. F., Trudgian, D. C., Mirzaei, H., Cobb, M. H. (2013). Regulation of OSR1 and the sodium, potassium, two chloride cotransporter by convergent signals, PNAS, 110 (47), 18826-18831.

Kwon, I., Kato, M., Xiang, S. H., Wu, L., Theodoropoulos, P., Mirzaei, H., Han, T., Xie, S. H., Corden, J. L., McKnight, S. L. (2013) Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains, Cell, 155 (5), 1049-1060.

Chang, K. H., Li, R., Kuri, B., Lotan, Y., Roehrborn, C. G., Liu, J. Y., Vessella, R., Nelson, P. S., Kapur, P., Guo, X. F., Mirzaei, H., Auchus, R. J., Sharifi, N. (2013) A Gain-of-Function Mutation in DHT Synthesis in Castration-Resistant Prostate Cancer, Cell, 154 (5), 1074-1084.

Laxman, S., Sutter, B. M., Wu, X., Kumar, S., Guo, X., Trudgian, D. C., … & Tu, B. P. (2013). Sulfur Amino Acids Regulate Translational Capacity and Metabolic Homeostasis through Modulation of tRNA Thiolation. Cell, 154(2), 416-429.

Sun, Q., Carrasco, Y. P., Hu, Y., Guo, X., Mirzaei, H., MacMillan, J., & Chook, Y. M. (2013). Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1. Proceedings of the National Academy of Sciences110(4), 1303-1308.

Zhang, L., Krachler, A. M., Broberg, C. A., Li, Y., Mirzaei, H., Gilpin, C. J., & Orth, K. (2012). Type III Effector VopC Mediates Invasion for Vibrio Species. Cell Reports1(5), 453-460.

Han TW, Kato M, Xie S, Wu LC, Mirzaei H, Pei J, Chen M, Xie Y, Allen J, Xiao G, McKnight SL. Cell-Free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell. 2012 May 11;149(4):768-79.

Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin NV, Frantz DE, Schneider JW, Chen S, Li L, Sawaya MR, Eisenberg D, Tycko R, McKnight SL. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell. 2012 May 11;149(4):753-67.

Publications & Expertise of Core Staff

The staff of the core have extensive knowledge of various aspects of proteomics, and have published widely on topics including:

  • Post-translational modifications (phosphorylation, ubiquitination, methylation, carbonylation, oxidation).
  • Targeted proteomics – SRM & MRM techniques and assays.
  • Quantitation – SILAC and label-free techniques.
  • Bioinformatics & data analysis.
  • Biomarker studies from clinical samples.
  • Standards and guidelines for the field.

As well as  providing fee-base and collaborative services the staff maintain their own research in projects. This ensures that the core is able to provide valuable advice and truly state-of-the art services to the UTSW community. A selection of staff publications are listed below:

H. Mirzaei, T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, D. J. Dilworth, J. K. Eng, J. D. Aitchison, I. Shmulevich, T. Galitski, R. Aebersold and J. Ranish, Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins, PNAS, Early Edition doi: 10.1073/pnas.1216918110, 2013.

D.C. Trudgian and H. Mirzaei, Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing, J. Proteome Research. EPub 2012 [Journal Link]

D.C. Trudgian, R. Singleton, M.E. Cockman, P.J. Ratcliffe and B.M. Kessler, ModLS: Post-Translational Modification Localization Scoring with Automatic Specificity Expansion. J. Proteomics and Bioinformatics. 5(12), 283-289, 2012. [Journal Link]

Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ.Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans.Nat Chem Biol. 2012 Dec;8(12):960-2

Uhlmann T, Geoghegan VL, Thomas B, Ridlova G, Trudgian DC, Acuto O. A Method for Large-scale Identification of Protein Arginine Methylation.Mol Cell Proteomics. 2012 Nov;11(11):1489-99

Fischer R, Trudgian DC, Wright C, Thomas G, Bradbury LA, Brown MA, Bowness P, Kessler BM.Discovery of candidate serum proteomic and metabolomic biomarkers in ankylosing spondylitis. Mol Cell Proteomics. 2012 Feb;11(2):M111.013904

D. C. Trudgian, G. Ridlova, R. Fischer, M. M. Mackeen, N. Ternette, O. Acuto, B. M. Kessler, and B. Thomas, Comparative Evaluation of Label-Free SINQ Normalized Spectral Index Quantitation in the Central Proteomics Facilities Pipeline, PROTEOMICS, 11(4), 2790-2797, 2011. [Journal Link]

D. C. Trudgian, B. Thomas, S. J. McGowan, B. M. Kessler, M. Salek and O. Acuto, CPFP: a central proteomics facilities pipeline, Bioinformatics, 26(8), pp. 1131-1132, 2010. [Journal Link]

Mirzaei, H.; Rogers, R.; Grimes, B.; Eng, J.; Aderem, A.; Aebersold, R. Characterizing the Connectivity of Poly-Ubiquitin Chains by Selected Reaction Monitoring Mass Spectrometry – Mol.BioSyst. 2010, 6(10), 2004

Jones, A.; Kathleen, C.; Knight, D.; MacLellan, K.; Domann, P.; Legido-Quigley, C.; Huang, L.;Smallshaw, L.; Mirzaei, H.; Shofstahl, J.; Paton, N. Guidelines for reporting the use of column chromatography in proteomics. – Nat. Biotechnol. 2010, 28(7), 654

Mirzaei, H.; Brusniak, M.; Mueller, L.; Letarte, S.; Watts, J.; Aebersold, R. Halogenated-Peptides as Internal Standards (H-PINS); Introduction of a MS-based internal standard set for liquid chromatography mass spectrometry – MCP, 2009, 8, 1934

Picotti, P.; Lam, H.; Campbell, D.; Deutsch, E.; Mirzaei, H.; Ranish, J.; Domon, B.; Aebersold R. A database of validated assays for the targeted mass spectrometric analysis of the S. cerevisiae proteome – Nat. Meth. 2008, 5, 913

Mirzaei, H.; McBee, J.; Watts J.; Aebersold R., Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics – MCP, 2008, 7, 813

Pierce, A.; Mirzaei, H.; Muller, F.; De Waal, E.; Taylor, A.; Leonard, S.; Van Remmen, H.; Regnier,F.; Richardson, A.; Chaudhuri, A.R. GAPDH is conformationally and functionally altered in association with oxidative stress in mouse models of amyotrophic lateral sclerosis–J. Mol. Biol. 2008,24, 382

Yang, W.-C.; Mirzaei, H.; Liu, X.; Regnier, F.; Enhancement of Amino Acid Detection and Quantification by Electrospray Ionization Mass Spectrometry- Anal. Chem., 2006; 78(13); 4702

Mirzaei, H.; Regnier, F., Enhancing Electrospray Ionization Efficiency of Peptides by Derivatization –Anal. Chem., 2006; 78(12); 4175

Mirzaei, H.; Schieler, J,; Roche, C,; Regnier, F.; Identification of Rotenone-Induced Modifications in α-Synuclein Using Affinity Pull-Down and Tandem Mass Spectrometry – Anal. Chem., 2006; 78(7); 2422

Mirzaei, H.; Regnier, F., Enrichment of Carbonylated Peptides Using Girard P Reagent and Strong Cation Exchange Chromatography – Anal. Chem., 2005, 78, (3), 770

Mirzaei, H.; Regnier, F., Affinity Chromatographic Selection of Carbonylated Proteins Followed by Identification of Oxidation Sites Using Tandem Mass Spectrometry – Anal. Chem. 2005, 77, (8), 2386

 

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