CBC Publications from Proteomics and informatics Services Facility (PISF)
Cho SH, Goodlett D, Franzblau S. ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis. Tuberculosis (Edinb). 2006 Nov;86(6):445-60. (PubMed)
Liu A, Pajkovic N, Pang Y, Zhu D, Calamini B, Mesecar AL, van Breemen RB. Absorption and subcellular localization of lycopene in human prostate cancer cells. Mol Cancer Ther. 2006 Nov;5(11):2879-85. (PubMed)
Silverstein JC, Ehrenfeld JM, Croft DA, Dech FW, Small S, Cook S. Tele-immersion: Preferred infrastructure for anatomy instruction. Journal of Computing in Higher Education, 2006 Volume 18, Number 1 / September: 80-93. (Download PDF)
Eggler AL, Luo Y, van Breemen RB, Mesecar AD. Identification of the highly reactive cysteine 151 in the chemopreventive agent-sensor Keap1 protein is method-dependent. Chem Res Toxicol. 2007 Dec;20(12):1878-84. (PubMed)
Fang F, Grossman R, Liu X. An Algorithm for Assigning Unique Keys to Metabolic Pathways. BIBM 2007. IEEE International Conference on Bioinformatics and Biomedicine. pp 374-382. (IEE Xplore)
Liu D, Guo J, Luo Y, Broderick DJ, Schimerlik MI, Pezzuto JM, van Breemen RB. Screening for ligands of human retinoid X receptor-alpha using ultrafiltration mass spectrometry. Anal Chem. 2007 Dec 15;79(24):9398-402. (PubMed)
Long F, McElheny D, Jiang S, Park S, Caffrey MS, Fung LW. Conformational change of erythroid alpha-spectrin at the tetramerization site upon binding beta-spectrin. Protein Sci. 2007 Nov;16(11):2519-30. (PubMed)
Luo Y, Eggler AL, Liu D, Liu G, Mesecar AD, van Breemen RB. Sites of alkylation of human Keap1 by natural chemoprevention agents. J Am Soc Mass Spectrom. 2007 Dec;18(12):2226-32. (PubMed)
Mody PD, Cannon JL, Bandukwala HS, Blaine KM, Schilling AB, Swier K, Sperling AI. Signaling through CD43 regulates CD4 T-cell trafficking. Blood. 2007 Oct 15;110(8):2974-82. (PubMed)
Murphy SC, Fernandez-Pol S, Chung PH, Prasanna Murthy SN, Milne SB, Salomao M, Brown HA, Lomasney JW, Mohandas N, Haldar K. Cytoplasmic remodeling of erythrocyte raft lipids during infection by the human malaria parasite Plasmodium falciparum. Blood. 2007 Sep 15;110(6):2132-9. (PubMed)
Sheahan KL, Cordero CL, Satchell KJ. Autoprocessing of the Vibrio cholerae RTX toxin by the cysteine protease domain. EMBO J., 2007 16; 26(10): 2552-61. (PubMed) (Download PDF)
Snyder JB, Nelson ME, Burdick JW, Maciver MA. Omnidirectional sensory and motor volumes in electric fish. PLoS Biol. 2007 Nov;5(11):e301. (PubMed) (Download PDF)
Vahebi S, Ota A, Li M, Warren CM, de Tombe PP, Wang Y, Solaro RJ. p38-MAPK induced dephosphorylation of alpha-tropomyosin is associated with depression of myocardial sarcomeric tension and ATPase activity. Circ Res. 2007 Feb 16;100(3):408-15. (PubMed)
Xiao L, Zhao Q, Du Y, Yuan C, Solaro RJ, Buttrick PM. PKC-epsilon increases phosphorylation of the cardiac myosin binding protein C at serine 302 both in vitro and in vivo. Biochemistry. 2007 Jun 12;46(23):7054-61. (PubMed)
Zhang Y, Brovkovych V, Brovkovych S, Tan F, Lee BS, Sharma T, Skidgel RA. Dynamic receptor-dependent activation of inducible nitric-oxide synthase by ERK-mediated phosphorylation of Ser745. J Biol Chem. 2007 Nov 2;282(44):32453-61. (PubMed)
Antoniou C, Fung LW. Potential artifacts in using a glutathione S-transferase fusion protein system and spin labeling electron paramagnetic resonance methods to study protein-protein interactions. Anal Biochem. 2008 May 1; 376(1): 160–162. (PubMed)
Antoniou C, Lam VQ, Fung LW. Conformational changes at the tetramerization site of erythroid alpha-spectrin upon binding beta-spectrin: a spin label EPR study. Biochemistry, 2008 Oct 7;47(40):10765-72. (PubMed)
Cao H, Xiao L, Park G, Wang X, Azim AC, Christman JW, van Breemen RB. An improved LC-MS/MS method for the quantification of prostaglandins E(2) and D(2) production in biological fluids. Anal Biochem. 2008 Jan 1;372(1):41-51. (PubMed)
Choi Y, van Breemen RB. Development of a screening assay for ligands to the estrogen receptor based on magnetic microparticles and LC-MS. Comb Chem High Throughput Screen. 2008 Jan;11(1):1-6. (PubMed)
Dietz BM, Liu D, Hagos GK, Yao P, Schinkovitz A, Pro SM, Deng S, Farnsworth NR, Pauli GF, van Breemen RB, Bolton JL. Angelica sinensis and Its Alkylphthalides Induce the Detoxification Enzyme NAD(P)H: Quinone Oxidoreductase 1 by Alkylating Keap1. Chem Res Toxicol. 2008. (PubMed)
Doan N, Gettins PG. alpha-Macroglobulins are present in some gram-negative bacteria: characterization of the alpha2-macroglobulin from Escherichia coli. J Biol Chem. 2008 Oct 17;283(42):28747-56. (PubMed)
Guo J, Liu A, Cao H, Luo Y, Pezzuto JM, van Breemen RB. Biotransformation of the chemopreventive agent 2',4',4-trihydroxychalcone (isoliquiritigenin) by UDP-glucuronosyltransferases. Drug Metab Dispos. 2008 Oct;36(10):2104-12. (PubMed)
Guo J, Liu D, Nikolic D, Zhu D, Pezzuto JM, van Breemen RB. In vitro metabolism of isoliquiritigenin by human liver microsomes. Drug Metab Dispos. 2008 Feb;36(2):461-8. (PubMed)
Kristjansdottir K, Wolfgeher D, Lucius N, Angulo DS, Kron SJ. Phosphoprotein profiling by PA-GeLC-MS/MS. J Proteome Res. 2008 Jul;7(7):2812-24. (PubMed)
Lee BS, Krishnanchettiar S, Lateef SS, Gupta S. Capturing biotinylated proteins and peptides by avidin functional affinity electrophoresis. Methods Mol Biol. 2008;418:51-62. (PubMed)
Lee BS, Lasanthi GD, Jayathilaka P, Huang JS, Gupta S. Immobilized metal affinity electrophoresis: a novel method of capturing phosphoproteins by electrophoresis. J Biomol Tech. 2008 Apr;19(2):106-8. (PubMed)
Morimoto RI. Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging. Genes Dev. 2008 Jun 1;22(11):1427-38. Review. (PubMed)
Parker L, Engel-Hall A, Drew K, Steinhardt G, Helseth DL Jr, Jabon D, McMurry T, Angulo DS, Kron SJ. Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. J Mass Spectrom. 2008 Apr;43(4):518-27. (PubMed)
Prahlad V, Cornelius T, Morimoto RI. Regulation of the cellular heat shock response in Caenorhabditis elegans by thermosensory neurons. Science. 2008 May 9;320(5877):811-4. (PubMed)
Prochazkova K, Satchell KJ. Structure-function analysis of inositol hexakisphosphate-induced autoprocessing of the Vibrio cholerae multifunctional autoprocessing RTX toxin. J Biol Chem. 2008 Aug 29;283(35):23656-64. (PubMed)
Rao PK, Rodriguez GM, Smith I, Li Q. Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-fourier transform mass spectrometry. Anal Chem. 2008 Sep 15;80(18):6860-9. (PubMed)
Rao PK, Roxas BA, Li Q. Determination of global protein turnover in stressed mycobacterium cells using hybrid-linear ion trap-fourier transform mass spectrometry. Anal Chem. 2008 Jan 15;80(2):396-406. (PubMed)
Ravindran S, Narayanan K, Eapen AS, Hao J, Ramachandran A, Blond S, George A. Endoplasmic reticulum chaperone protein GRP-78 mediates endocytosis of dentin matrix protein 1. J Biol Chem. 2008 Oct 31;283(44):29658-70. (PubMed)
Roxas BA, Li Q. Significance analysis of microarray for relative quantitation of LC/MS data in proteomics. BMC Bioinformatics. 2008 Apr 10;9:187. (PubMed)
Ulanovskaya OA, Janjic J, Suzuki M, Sabharwal SS, Schumacker PT, Kron SJ, Kozmin SA. Synthesis enables identification of the cellular target of leucascandrolide A and neopeltolide. Nat Chem Biol. 2008 Jul;4(7):418-24. (PubMed)
Warren CM, Arteaga GM, Rajan S, Ahmed RP, Wieczorek DF, Solaro RJ. Use of 2-D DIGE analysis reveals altered phosphorylation in a tropomyosin mutant (Glu54Lys) linked to dilated cardiomyopathy. Proteomics. 2008 Jan;8(1):100-5. (PubMed)
Yuan C, Sheng Q, Tang H, Li Y, Zeng R, Solaro RJ. Quantitative comparison of sarcomeric phosphoproteomes of neonatal and adult rat hearts. Am J Physiol Heart Circ Physiol. 2008 Aug;295(2):H647-56. (PubMed)
Yuan C, Solaro RJ. Myofilament proteins: From cardiac disorders to proteomic changes. 2008. Proteomics Clin Appl 2: 788-799. (InterScience)
Abdul-Hay SO, Edirisinghe P, Thatcher GR. Selective modulation of amyloid-beta peptide degradation by flurbiprofen, fenofibrate, and related compounds regulates Abeta levels. J Neurochem. 2009 Nov;111(3):683-95. (PubMed)
Abdul-Hay SO, Luo J, Ashghodom RT, Thatcher GR. NO-flurbiprofen reduces amyloid-beta, is neuroprotective in cell culture, and enhances cognition in response to cholinergic blockade. J Neurochem. 2009 Nov;111(3):766-76. (PubMed)
He B, Velaparthi S, Pieffet G, Pennington C, Mahesh A, Holzle DL, Brunsteiner M, van Breemen R, Blond SY, Petukhov PA. Binding ensemble profiling with photoaffinity labeling (BEProFL) approach: mapping the binding poses of HDAC8 inhibitors. J Med Chem. 2009 Nov 26;52(22):7003-13. (PubMed)
Li Q, Fung LW. Structural and dynamic study of the tetramerization region of non-erythroid alpha-spectrin: a frayed helix revealed by site-directed spin labeling electron paramagnetic resonance. Biochemistry. 2009 Jan 13;48(1):206-15. (PubMed)
Li Q, Roxas BA. An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters. BMC Bioinformatics. 2009 Feb 2;10:43. (PubMed)
Manolopoulou M, Guo Q, Malito E, Schilling AB, Tang WJ. Molecular basis of catalytic chamber-assisted unfolding and cleavage of human insulin by human insulin-degrading enzyme. J Biol Chem. 2009 May 22;284(21):14177-88. (PubMed)
Nakahata Y, Sahar S, Astarita G, Kaluzova M, Sassone-Corsi P. Circadian control of the NAD+ salvage pathway by CLOCK-SIRT1 Science. 2009 May 1;324(5927):654-7. (PubMed)
Poor CB, Chen PR, Duguid E, Rice PA, He C. Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus. J Biol Chem. 2009 Aug 28;284(35):23517-24. (PubMed)
Prahlad V, Morimoto RI. Integrating the stress response: lessons for neurodegenerative diseases from C. elegans. Trends Cell Biol. 2009 Feb;19(2):52-61. Review. (PubMed)
Prochazkova K, Shuvalova LA, Minasov G, Voburka Z, Anderson WF, Satchell KJ. Structural and molecular mechanism for autoprocessing of MARTX toxin of Vibrio cholerae at multiple sites. J Biol Chem. 2009 Sep 25;284(39):26557-68. (PubMed)
Qin Z, Kastrati I, Ashgodom RT, Lantvit DD, Overk CR, Choi Y, van Breemen RB, Bolton JL, Thatcher GR. Structural modulation of oxidative metabolism in design of improved benzothiophene selective estrogen receptor modulators. Drug Metab Dispos. 2009 Jan;37(1):161-9. (PubMed)
Ralat LA, Ren M, Schilling AB, Tang WJ. Protective role of Cys-178 against the inactivation and oligomerization of human insulin-degrading enzyme by oxidation and nitrosylation. J Biol Chem. 2009 Dec 4;284(49):34005-18. (PubMed)
Rao PK, Li Q. Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis. J Proteomics Bioinform. 2009 Jan 15;2(1):19-31. (PubMed)
Rao PK, Li Q. Protein Turnover in Mycobacterial Proteomics. Molecules. 2009 14(9), 3237-3258. (mdpi)
Rao PK, Singh CR, Jagannath C, Li Q. Phagosomal proteomes modulated by mycobacterial infections. Int J Clin Exp Med. 2009 2(3):233-247. (ijcem)
Roxas BA, Li Q. Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis. Int J Clin Exp Med. 2009 Nov 10;2(4):309-28. (PubMed)
Song Y, Pipalia NH, Fung LW. The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin. Protein Sci. 2009 Sep;18(9):1916-25. (PubMed)
Volchenboum SL, Kristjansdottir K, Wolfgeher D, Kron SJ. Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns. Mol Cell Proteomics. 2009 Aug;8(8):2011-22. (PubMed)
Warren CM, Kobayashi T, Solaro RJ. Sites of intra- and intermolecular cross-linking of the N-terminal extension of troponin I in human cardiac whole troponin complex. J Biol Chem. 2009 May 22;284(21):14258-66. (PubMed)
Westerheide SD, Anckar J, Stevens SM Jr, Sistonen L, Morimoto RI. Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1. Science. 2009 Feb 20;323(5917):1063-6. (PubMed) (Download PDF)
Xu H, Freitas MA. Automated diagnosis of LC-MS/MS performance. Bioinformatics. 2009 May 15;25(10):1341-3. (PubMed)
Xu H, Freitas MA. MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data. Proteomics. 2009 Mar;9(6):1548-55. (PubMed)
Xu H, Wang L, Sallans L, Freitas MA. A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra. Proteomics. 2009 Apr;9(7):1763-70. (PubMed)
Yu B, Qin Z, Wijewickrama GT, Edirisinghe P, Bolton JL, Thatcher GR. Comparative methods for analysis of protein covalent modification by electrophilic quinoids formed from xenobiotics. Bioconjug Chem. 2009 Apr;20(4):728-41. (PubMed)
Zhao J, Camp SM, Chiang ET, Schilling AB, Dudek SM, Garcia JGN. Identification of novel in vitro protein kinase A phosphorylation sites on recombinant non-muscle myosin light chain kinase: nano-liquid chromatography tandem mass spectrometry methodology. J of Organ Dysfunction. 2009, Vol. 5, No. 4:242-253. (J of Organ Dysfunction)
Zhao J, Singleton PA, Brown ME, Dudek SM, Garcia JG. Phosphotyrosine protein dynamics in cell membrane rafts of sphingosine-1-phosphate-stimulated human endothelium: role in barrier enhancement. Cell Signal. 2009 Dec;21(12):1945-60. (PubMed)
Alonzo F 3rd, Freitag NE. Listeria monocytogenes PrsA2 is required for virulence factor secretion and bacterial viability within the host cell cytosol. Infect Immun. 2010 Nov;78(11):4944-57. (PubMed)
Alvarez HM, Xue Y, Robinson CD, Canalizo-Hernández MA, Marvin RG, Kelly RA, Mondragón A, Penner-Hahn JE, O'Halloran TV. Tetrathiomolybdate Inhibits Copper Trafficking Proteins Through Metal Cluster Formation. Science. 2010 Jan 15;327(5963):331-4. (PubMed)
Dong L, Shion H, Davis RG, Terry-Penak B, Castro-Perez J, van Breemen RB. Collision Cross-Section Determination and Tandem Mass Spectrometric Analysis of Isomeric Carotenoids Using Electrospray Ion Mobility Time-of-Flight Mass Spectrometry. Anal Chem. 2010, 82 (21): 9014–9021. (PubMed)
Gerbasi VR, Golden DE, Hurtado SB, Sontheimer EJ. Proteomic identification of Drosophila siRNA-associated factors. Mol Cell Proteomics. 2010 Sep;9(9):1866-72. (PubMed)
Guo Q, Manolopoulou M, Bian Y, Schilling AB, Tang WJ. Molecular basis for the recognition and cleavages of IGF-II, TGF-alpha, and amylin by human insulin-degrading enzyme. J Mol Biol. 2010 Jan 15;395(2):430-43. (PubMed)
Han MH, Lin C, Meng S, Wang X. Proteomics analysis reveals overlapping functions of clustered protocadherins. Mol Cell Proteomics. 2010 Jan;9(1):71-83. (PubMed)
Jelenska J, van Hal JA, Greenberg JT. Pseudomonas syringae hijacks plant stress chaperone machinery for virulence. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13177-82. (PubMed)
Kang J, Song Y, Sevinc A, Fung LW. Important residue (G46) in erythroid spectrin tetramer formation. Cell Mol Biol Lett. 2010;15(1):46-54. (PubMed)
Källberg M, Lu H. An improved machine learning protocol for the identification of correct Sequest search results. BMC Bioinformatics. 2010 Dec 7;11:591. (PubMed)
Kern J, Ryan C, Faull K, Schneewind O. Bacillus anthracis surface-layer proteins assemble by binding to the secondary cell wall polysaccharide in a manner that requires csaB and tagO. J Mol Biol. 2010 Sep 3;401(5):757-75. (PubMed)
Kowlessur D, Tobacman LS. Low temperature dynamic mapping reveals unexpected order and disorder in troponin. J Biol Chem. 2010 Dec 10;285(50):38978-86. (PubMed)
Kowlessur D, Tobacman LS. Troponin Regulatory Function and Dynamics Revealed by H/D Exchange-Mass Spectrometry. J Biol Chem. 2010 Jan 22;285(4):2686-2694. (PubMed)
Kroes RA, He H, Emmett MR, Nilsson CL, Leach FE 3rd, Amster IJ, Marshall AG, Moskal JR. Overexpression of ST6GalNAcV, a ganglioside-specific alpha2,6-sialyltransferase, inhibits glioma growth in vivo. Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12646-51. (PubMed)
Li Q. Advances in protein turnover analysis at the global level and biological insights. Mass Spectrom Rev. 2010 Sep;29(5):717-36. (PubMed)
Li Q. Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates. International Journal of Proteomics. 2010 Vol 2010, Article ID 731582, 15 pages. (Online)
Li Q, Jagannath C, Rao PK, Singh CR, Lostumbo G. Analysis of phagosomal proteomes: From latex-bead to bacterial phagosomes. Proteomics. 2010 Nov;10(22):4098-4116. doi: 10.1002/pmic.201000210. (PubMed)
Li Q, Lostumbo G. Proteomic Analyses of a Variety of Intracellular Bacterial Species Infecting Different Host Cell Lines. Current Proteomics, Volume 7, Number 3, October 2010 , pp. 222-232(11). (Online)
Markaryan A, Nelson EG, Helseth LD, Hinojosa R. Proteomic analysis of formalin-fixed celloidin-embedded whole cochlear and laser microdissected spiral ganglion tissues. Acta Otolaryngol. 2010 Sep;130(9):984-9. (PubMed)
Mehboob S, Song Y, Witek M, Long F, Santarsiero BD, Johnson ME, Fung LW. Crystal structure of the nonerythroid alpha-spectrin tetramerization site reveals differences between erythroid and nonerythroid spectrin tetramer formation. J Biol Chem. 2010 May 7;285(19):14572-84. (PubMed)
Musch MW, Arvans DL, Wang Y, Nakagawa Y, Solomaha E, Chang EB. Cyclic AMP-mediated endocytosis of intestinal epithelial NHE3 requires binding to synaptotagmin 1. Am J Physiol Gastrointest Liver Physiol. 2010 Feb;298(2):G203-11. (PubMed)
Plant LD, Dementieva IS, Kollewe A, Olikara S, Marks JD, Goldstein SA. One SUMO is sufficient to silence the dimeric potassium channel K2P1. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10743-8. (PubMed)
Ren M, Guo Q, Guo L, Lenz M, Qian F, Koenen RR, Xu H, Schilling AB, Weber C, Ye RD, Dinner AR, Tang WJ. Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme. EMBO J. 2010 Dec 1;29(23):3952-66. (PubMed)
Scruggs SB, Reisdorph R, Armstrong ML, Warren CM, Reisdorph N, Solaro RJ, Buttrick PM. A novel, in-solution separation of endogenous cardiac sarcomeric proteins and identification of distinct charged variants of regulatory light chain. Mol Cell Proteomics. 2010 Sep;9(9):1804-18. (PubMed)
Sinha V, Wijewickrama GT, Chandrasena RE, Xu H, Edirisinghe PD, Schiefer IT, Thatcher GR. Proteomic and Mass Spectroscopic Quantitation of Protein S-Nitrosation Differentiates NO-Donors. ACS Chem Biol. 2010 Jul 16;5(7):667-80. (PubMed)
Spruell, JM, Coskun, A, Friedman, DC, Forgan, RS, Sarjeant, AA, Trabolsi, A, Fahrenbach, AC, Barin, G, Paxton, WF, Dey, SK, Olson, MA, Benítez, D, Tkatchouk, E, Colvin, MT, Carmielli, R, Caldwell, ST, Rosair, GM, Hewage, SG, Duclairoir, F, Seymour, JL, Slawin, AMZ, Goddard III, WA, Wasielewski, MR, Cooke, G, and Stoddart, JF. Highly stable tetrathiafulvalene radical dimers in [3]catenanes. Nat Chem. Nat Chem. 2010 Oct;2(10):870-9. (PubMed)
Todorovic V, Desai BV, Eigenheer RA, Yin T, Amargo EV, Mrksich M, Green KJ, Patterson MJ. Detection of differentially expressed Basal cell proteins by mass spectrometry. Mol Cell Proteomics. 2010 Feb;9(2):351-61. (PubMed)
Warren CM, Geenen DL, Helseth DL Jr, Xu H, Solaro RJ. Sub-proteomic fractionation, iTRAQ, and OFFGEL-LC-MS/MS approaches to cardiac proteomics. J Proteomics. 2010 Jun 16;73(8):1551-61. (PubMed)
Wu D, Sylvester JE, Parker LL, Zhou G, Kron SJ. Peptide reporters of kinase activity in whole cell lysates. Biopolymers. 2010;94(4):475-86. (PubMed)
Xu H, Freitas MA. A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra. BMC Bioinformatics 2010 11:436. (biomedcentral)
Xu H, Hsu PH, Zhang L, Tsai MD, Freitas MA. Database Search Algorithm for Identification of Intact Cross-Links in Proteins and Peptides Using Tandem Mass Spectrometry. J Proteome Res. 2010 Jul 2;9(7):3384-93. (PubMed)
Yang L, Tu S, Ren C, Bulloch EM, Liao CL, Tsai MD, Freitas MA. Unambiguous determination of isobaric histone modifications by reversed-phase retention time and high-mass accuracy. Anal Biochem. 2010 Jan 1;396(1):13-22. (PubMed)
Aguirre B, Costas M, Cabrera N, Mendoza-Hernández G, Helseth DL Jr, Fernández P, Tuena de Gómez-Puyou M, Pérez-Montfort R, Torres-Larios A, Gómez-Puyou A. A Ribosomal Misincorporation of Lys for Arg in Human Triosephosphate Isomerase Expressed in Escherichia coli Gives Rise to Two Protein Populations. PLoS ONE. 2011 6(6): e21035. doi:10.1371/journal.pone.0021035 (PLoS ONE)
Avner BS, Shioura KM, Scruggs SB, Grachoff M, Geenen DL, Helseth DL Jr, Farjah M, Goldspink PH, Solaro JR. Myocardial infarction in mice alters sarcomeric function via post-translational protein modification. Mol Cell Biochem. 2011 Dec 8. [Epub ahead of print] (PubMed)
Chen P, Lingen M, Sonis ST, Walsh-Reitz MM, Toback FG. Role of AMP-18 in oral mucositis. Oral Oncol. 2011 Sep;47(9):831-9. (PubMed)
Ferreira A, Bigio EH. Calpain-mediated tau cleavage: a mechanism leading to neurodegeneration shared by multiple tauopathies. Mol Med. 2011;17(7-8):676-85. (PubMed)
García J. The calcium channel α2/δ1 subunit interacts with ATP5b in the plasma membrane of developing muscle cells. Am J Physiol Cell Physiol. 2011 Jul;301(1):C44-52. (PubMed)
Gerbasi VR, Preall JB, Golden DE, Powell DW, Cummins TD, Sontheimer EJ. Blanks, a nuclear siRNA/dsRNA-binding complex component, is required for Drosophila spermiogenesis. Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3204-9. (PubMed)
Hu C, Eggler AL, Mesecar AD, van Breemen RB. Modification of Keap1 Cysteine Residues by Sulforaphane. Chem Res Toxicol. 2011 Apr 18;24(4):515-21. (PubMed)
Kowal AS, Chisholm RL. Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion. Eukaryot Cell. 2011 May;10(5):662-71. (PubMed)
Kuzmis A, Lim SB, Desai E, Jeon E, Lee BS, Rubinstein I, Onyüksel H. Micellar nanomedicine of human neuropeptide Y. Nanomedicine. 2011 Aug;7(4):464-71. (PubMed)
Lee BS, Jayathilaka GD, Huang JS, Vida LN, Honig GR, Gupta S. Analyses of in vitro nonenzymatic glycation of normal and variant hemoglobins by maldi-tof mass spectrometry. J Biomol Tech. 2011 Sep;22(3):90-4. (PubMed)
Li Q. Precision Quantitative Proteomics with Fourier-Transform Mass Spectrometry. (Chapter) In: Fourier Transforms - New Analytical Approaches and FTIR Strategies). Publisher: InTech, April 2011. (InTech)
Li Q, Singh CR, Ma S, Price ND, Jagannath C. Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages. J Proteome Res. 2011 May 6;10(5):2425-39. (PubMed)
Pronier E, Almire C, Mokrani H, Vasanthakumar A, Simon A, da Costa Reis Monte Mor B, Massé A, Le Couédic JP, Pendino F, Carbonne B, Larghero J, Ravanat JL, Casadevall N, Bernard OA, Droin N, Solary E, Godley LA, Vainchenker W, Plo I, Delhommeau F. Inhibition of TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine disturbs erythroid and granulomonocytic differentiation of human hematopoietic progenitors. Blood. 2011 Sep 1;118(9):2551-5. (PubMed)
Ralat LA, Guo Q, Ren M, Funke T, Dickey DM, Potter LR, Tang WJ. Insulin-degrading enzyme modulates the natriuretic peptide- mediated signaling response. J Biol Chem. 2011 Feb 11;286(6):4670-9. (PubMed)
Ralat LA, Kalas V, Zheng Z, Goldman RD, Sosnick TR, Tang WJ. Ubiquitin is a novel substrate for human insulin-degrading enzyme. J Mol Biol. 2011 Feb 25;406(3):454-66. (PubMed)
Schiefer IT, Abdul-Hay S, Wang H, Vanni M, Qin Z, Thatcher GR. Inhibition of Amyloidogenesis by Nonsteroidal Anti-inflammatory Drugs and Their Hybrid Nitrates. J Med Chem. 2011 Apr 14;54(7):2293-306. (PubMed)
Woloszynska-Read A, Zhang W, Yu J, Link PA, Mhawech-Fauceglia P, Collamat G, Akers SN, Ostler KR, Godley LA, Odunsi K, Karpf AR. Coordinated Cancer Germline Antigen Promoter and Global DNA Hypomethylation in Ovarian Cancer: Association with the BORIS/CTCF Expression Ratio and Advanced Stage. Clin Cancer Res. 2011 Apr 15;17(8):2170-80. (PubMed)
Hu C, Nikolic D, Eggler AL, Mesecar AD, van Breemen RB. Screening for natural chemoprevention agents that modify human Keap1. Anal Biochem. 2012 Feb 1;421(1):108-14. (PubMed)
Posters presented by members of our facility at the annual meeting of the American Society for Mass Spectrometry in Salt Lake City, UT, May 24-27, 2010:
Alexander B. Schilling, Carrie Crot, Larry Helseth, Rod Davis and Hua Xu. Conversion of an Agilent Chip Cube system for the analysis of proteomics samples using a LTQ-FT Ultra mass spectrometer.
Roderick Davis, Jia You, Michael A. Freitas and Hua Xu. Middle-Down Proteomics with High Mass Accuracy Tandem Mass Spectrometry and Mass Accuracy Sensitive Database Search Engine.
Pang-Hung Hsu, Liwen Zhang, Michael A. Freitas, and Hua Xu. Automated Quantitative Analysis of LC-MS/MS Data with Isobaric Tags or Stable Isotope Labeling in MassMatrix Database Search Engine.
Hua Xu, Pang-Hung Hsu, Roderick Davis, Ming-Daw Tsai and Michael A. Freitas. A Universal Search Algorithm for Identification of Selective/Nonselective Cross-Links in Proteins Using Tandem Mass Spectrometry.
Poster presented by members of our facility at the annual meeting of the Association for Biomolecular Research Facilities in Sacramento, CA, March 20-23, 2010:
Schilling, AB, Crot C, Helseth L, Xu, H., Davis, RG. Conversion of an Agilent Chip Cube system and adaptation of a ROXY EC potentiostat for the analysis of proteolytic and non-proteolytic protein samples on a Thermo Finnigan LTQ-FT Ultra mass spectrometer.
Posters presented by the Proteomics Facility at the annual meeting of the Association for Biomolecular Research Facilities in Memphis, TN, Feb 7-10, 2009:
Helseth DL Jr, Xu H, Schilling AB. Automating Commercial Mass Spectrometry Search Engines, poster SR42-S2
Xu H, Helseth DL Jr, Schilling AB, Freitas MA. A Free Web-Based Database Search Engine for Tandem Mass Spectrometric Data of Proteins and Peptides, poster SR47-S2
Helseth DL Jr, Xu H, Hendrickson B, Schilling AB. The CBC/RRC Proteomics and Informatics Services Facility at UIC, poster CF33-M
Posters presented by the facility at the annual meeting of the American Society for Mass Spectrometry in Philadelphia, May 31-June 4, 2009:
Xu H, Hsu P, Zhang L, Freitas MA. A Database Search Algorithm for Identification of Intact Cross links in Proteins and Peptides Using Tandem Mass Spectrometry.
Martinez-Garriga B, Xu H, Kannan K, Mankin A. The role of nascent peptide-ribosome interactions in gene regulation using quantitative mass spectrometry with 15N-stable isotope labeling.
Dong L, Davis R, van Breemen RB. Separation of isomeric carotenoids using atmospheric pressure chemical ionization ion mobility spectometry-time-of-flight mass spectrometry.