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Facility Publications:

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." PDF
  • 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" PDF
  • 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" PDF
  • Linlin Dong, Henry Y. Shion, Roderick Davis, Brent Terry-Penak and Richard B. van Breemen, "Collision cross-section determination of isomeric carotenoids using electrospray ion mobility time-of-flight mass spectrometry" PDF

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." Abstract

Posters presented by members of our facility at the annual meeting of the American Society for Mass Spectrometry in Philadelphia, PA, May 31-June 4th, 2009:

  • Hua Xu; Pang-hung Hsu; Liwen Zhang; Michael A. Freitas, "A Database Search Algorithm for Identification of Intact Cross links in Proteins and Peptides Using Tandem Mass Spectrometry"
  • Blanca Martinez-Garriga, Hua Xu, Krishna Kannan, Alexander Mankin, "The role of nascent peptide-ribosome interactions in gene regulation using quantitative mass spectrometry with 15N-stable isotope labeling"
  • Linlin Dong, Roderick Davis, Richard B. van Breemen, "Separation of isomeric carotenoids using atmospheric pressure chemical ionization ion mobility spectometry-time-of-flight mass spectrometry"

Posters presented by members of our facility at the annual meeting of the Association for Biomolecular Research Facilities in Memphis, TN, Feb 7-10, 2009:

  • D.L. Helseth Jr., H. Xu, A.B. Schilling, "Automating Commercial Mass Spectrometry Search Engines", poster SR42-S2 (This poster describes our automated workflow) PDF
  • H. Xu, D.L. Helseth Jr., A.B. Schilling, M.A. Freitas, "A Free Web-Based Database Search Engine for Tandem Mass Spectrometric Data of Proteins and Peptides", poster SR47-S2 (this describes enhancements to the MassMatrix search engine including the N15/N14 quantitation software developed at our facility)
  • D.L. Helseth Jr., H. Xu, B. Hendrickson, A.B. Schilling, "The CBC/RRC Proteomics and Informatics Services Facility at UIC", poster CF33-M (Core Facility poster)

Publications from work performed at Proteomics Services (facility members in bold):
  1. Song Y, Kirkpatrick LL, Schilling AB, Helseth DL, Chabot N, Keillor JW, Johnson GV, Brady ST. "Transglutaminase and polyamination of tubulin: posttranslational modification for stabilizing axonal microtubules." Neuron. 2013 Apr 10;78(1):109-23. PMID: 23583110
  2. Kung VL, Khare S, Stehlik C, Bacon EM, Hughes AJ, Hauser AR. "An rhs gene of Pseudomonas aeruginosa encodes a virulence protein that activates the inflammasome." Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1275-80. PMID: 22232685
  3. Sabherwal Y, Mahajan N, Helseth DL, Gassmann M, Shi H, Zhang M. "PDEF downregulates stathmin expression in prostate cancer." Int J Oncol. 2012 Feb 29. doi: 10.3892/ijo.2012.1392. [Epub ahead of print] PMID: 22378487
  4. Klaic, L, Morimoto, RI, and Silverman, RB "Celastrol Analogs as Inducers of the Heat Shock Response. Design and Synthesis of Affinity Probes for the Identification of Protein Targets" ACS Chem. Biol., Just Accepted Manuscript, Publication Date (Web): March 1, 2012, DOI: 10.1021/cb200539u
  5. Vranceanua, F, Perkinsb, GA, Teradab, M, Chidavaenzia, RL, Ellismanb, MH and Lysakowski, A. "Striated organelle, a cytoskeletal structure positioned to modulate hair-cell transduction" Proc. Natl. Acad. Sci., Published online before print March 6, 2012, doi: 10.1073/pnas.1101003109
  6. Avner BS, Shioura KM, Scruggs SB, Grachoff M, Geenen DL, Helseth DL Jr, Farjah M, Goldspink PH, John Solaro R. "Myocardial infarction in mice alters sarcomeric function via post-translational protein modification." Mol Cell Biochem. 2011 Dec 8. [Epub ahead of print] PMID: 22160857
  7. Hu C, Nikolic D, Eggler AL, Mesecar AD, van Breemen RB. "Screening for natural chemoprevention agents that modify human Keap1." Anal Biochem. 2011 Oct 22. [Epub ahead of print] PMID: 22074792
  8. 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. PMID: 21966256
  9. 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. PMID: 21490313
  10. 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. PMID: 21737340
  11. 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. Epub 2011 Jan 25. PMID: 21272667
  12. 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 granulo-monocytic differentiation of human hematopoietic progenitors."  Blood, 2011 Jul 6. [Epub ahead of print]  PMID: 21734233
  13. Aguirre, B, Costas, M, Cabrera, N, Guillermo Mendoza-Hernández, G, Helseth, DL, Fernández, P, de Gómez-Puyou, MT, Pérez-Montfort, R, Torres-Larios, A and Gómez Puyou, AG. "A ribosomal misincorporation of Lys for Arg in human triosephosphate isomerase expressed in Escherichia coli gives rise to two protein populations." PLoS ONE 6(6): e21035. doi:10.1371/journal.pone.0021035
  14. Li Q. Precision Quantitative Proteomics with Fourier-Transform Mass Spectrometry, Fourier Transforms - New Analytical Approaches and FTIR Strategies, Goran Nikolic (Ed.), ISBN: 978-953-307-232-6, InTech, Vienna, 2011. Available through open access
  15. 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., Just Accepted Manuscript Publication Date (Web): March 17, 2011 doi/abs/10.1021/pr101245u
  16. 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 Mar 15. [Epub ahead of print] PMID: 21405086
  17. Woloszynska-Read A, Zhang W, Yu J, Link PA, Mhawech-Fauceglia P, Collamat G, Akers SN, Ostler KR, Godley LA, Odunsi KO, Karpf AR. "Coordinated cancer germline antigen promoter and global DNA hypomethylation in ovarian cancer: association with BORIS/CTCF expression ratio and advanced stage." Clin Cancer Res. 2011 Feb 4. [Epub ahead of print] PMID: 21296871
  18. Hu C, Eggler AL, Mesecar AD, van Breemen RB. "Modification of Keap1 Cysteine Residues by Sulforaphane." Chem Res Toxicol. 2011 Mar 10. [Epub ahead of print] PMID: 21391649
  19. Källberg M, Lu H. "An improved machine learning protocol for the identification of correct Sequest search results." BMC Bioinformatics. 2010 Dec 7;11:591. PMID: 21138573
  20. 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 7. PMID: 21300896
  21. Gupta S, Lasanthi GD, Jayathilaka F, Huang JS, Lee BS. "Two-dimensional immobilized metal affinity electrophoresis for capturing a phosphoprotein." J Biomol Tech. 2010 Dec;21(4):160-2. PMID: 21119927
  22. 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. PMID: 20959807
  23. Li, Q. "Advances in protein turnover analysis at the global level and biological insights." Mass Spectrom Rev. 2010 Sep;29(5):717-36. PMID: 19757418
  24. 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. PMID: 19756397
  25. 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. PMID: 20228407
  26. 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 Oct 7. [Epub ahead of print] PMID: 20939506
  27. Kowlessur D, Tobacman LS, "Low temperature dynamic mapping reveals unexpected order and disorder in troponin." J Biol Chem. Dec 10;285(50):38978-86. Epub 2010 Oct 2. PMID: 20889975
  28. 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. Epub 2010 Jul 13. PMID: 20603129
  29. 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. PMID: 20593469
  30. Li., Q., C. Jagannath, Rao, P. K., C. R. Singh, G. Lostumbo. "Analysis of Phagosomal proteomes: from latex-bead to bacterial phagosomes." Proteomics 2010. in press
  31. Li, Q. and G. Lostumbo. "Proteomic analyses of a variety of intracellular bacterial species infecting different host cell lines." Current Proteomics 2010, 5(3): in press.
  32. Li, Q. "Assigning significance in label-free quantitative proteomics to include single-peptide-hit proteins with low replicates." Int J Proteomics 2010, 2010(731582): 1-15.
  33. Xu H and Freitas MA, "A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra" BMC Bioinformatics 2010, 11:436 doi:10.1186/1471-2105-11-436
  34. Todorović 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. PMID: 19955077
  35. 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" Nature Chemistry (2010) doi:10.1038/nchem.749 Published online 25 July 2010
  36. 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. Epub 2010 May 24. PMID: 20498050
  37. Kroes, RA, He, H, Emmett, MR, Nilssond, CL, Leach III, FE, Amstere, IJ, Marshall, AG, and Moskal, JR. "Overexpression of ST6GalNAcV, a ganglioside-specific α2,6-sialyltransferase, inhibits glioma growth in vivo" Proc. Natl. Acad. Sci., Published online before print June 28, 2010, doi: 10.1073/pnas.0909862107
  38. 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 Jun 16. [Epub ahead of print] PMID: 20524644
  39. 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 May 24. [Epub ahead of print] PMID: 20498050
  40. Gerbasi VR, Golden DE, Hurtado SB, Sontheimer EJ, "Proteomic identification of Drosophila siRNA-associated factors." Mol Cell Proteomics. 2010 May 15. [Epub ahead of print] PMID: 20472918
  41. Xu, H, Hsu, P-H, Zhang, L, Tsai M-D and Freitas, MA, "A Database Search Algorithm for Identification of Intact Cross-Links in Proteins and Peptides Using Tandem Mass Spectrometry", J. Proteome Res., Just Accepted Manuscript DOI: 10.1021/pr100369y Publication Date (Web): May 15, 2010
  42. 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. Epub 2009 Oct 20. PMID: 19843561
  43. Scruggs, SB, Reisdorph, R, Armstrong, ML, Warren, CM, Reisdorph, N, Solaro, RJ and Buttrick, PM, "A Novel, In-Solution Separation of Endogenous Cardiac Sarcomeric Proteins and Identification of Distinct Charged Variants of Regulatory Light Chain" Molecular & Cellular Proteomics (in press) First Published on May 5, 2010, doi: 10.1074/mcp.M110.000075
  44. Warren, CM, Geenen, DL, Helseth, DL, Xu, H and Solaro, RJ. "Sub-Proteomic fractionation, iTRAQ, and OFFGEL-LC-MS/MS approaches to cardiac proteomics" J. Proteomics, 2010, [Epub ahead of print} PMID: 20394843
  45. Markaryan A, Nelson EG, Helseth DL, Hinojosa R., "Proteomic analysis of formalin-fixed celloidin-embedded whole cochlear and laser microdissected spiral ganglion tissues.", Acta Otolaryngol. 2010 Feb 12. [Epub ahead of print] PMID: 20148753
  46. 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. Epub 2009 Nov 19. PMID: 19926819
  47. Zhuo P, Goldberg M, Herman L, Lee BS, Wang H, Brown RL, Foster CB, Peters U, Diamond AM. "Molecular consequences of genetic variations in the glutathione peroxidase 1 selenoenzyme." Cancer Res. 2009 Oct 15;69(20):8183-90. Epub 2009 Oct 13. PMID: 19826042
  48. 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. PMID: 19886628
  49. 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. 2009 Nov 26. [Epub ahead of print] PMID: 19965379
  50. 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. PMID: 19321456
  51. Kowlessur D, Tobacman LS, "Troponin regulatory function and dynamics revealed by H/D exchange-mass spectrometry." J Biol Chem. 2009 Nov 17. [Epub ahead of print] PMID: 19920153
  52. 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. Epub 2009 Sep 13. PMID: 19755153
  53. 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. 2009 Nov 5. [Epub ahead of print] PMID: 19896952.
  54. 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 Oct 6. [Epub ahead of print] PMID: 19808678
  55. Roxas, B. and Q. Li, "Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis." International Journal of Clinical and Experimental Medicine 2 (2009):309-328
  56. Abdul-Hay SO, Edirisinghe P, Thatcher GR. 2009 "Selective modulation of amyloid-beta peptide degradation by flurbiprofen, fenofibrate, and related compounds regulates Abeta levels." J Neurochem. 2009 Nov;111(3):683-95. Epub 2009 Aug 22. PMID: 19702658
  57. Abdul-Hay SO, Luo J, Ashghodom RT, Thatcher GR. 2009 "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. Epub 2009 Aug 21. PMID: 19702655
  58. Rao, P. K., C. R. Singh, C. Jagannath, and Q. Li. 2009. "A systems biology approach to study the phagosomal proteome modulated by mycobacterial infections." International Journal of Clinical and Experimental Medicine 2:233-247  PMID: 19918316.
  59. Rao, P. K. and Q. Li. 2009. "Protein turnover in mycobacterial proteomics." Molecules 14:3237-3258 (Published in the special issue Neglected Diseases: Medicinal Chemistry and Natural Product Chemistry).  PMID: 19783922.
  60. Li Q, Mass Spectrom Rev. 2009 Sep 15 [Epub ahead of print], "Advances in protein turnover analysis at the global level and biological insights." PMID: 19757418
  61. Poor CB, Chen PR, Duguid E, Rice PA, He C., J Biol Chem. 2009 Aug 28;284(35):23517-24., "Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus." PMID: 19586910
  62. Yu B, Qin Z, Wijewickrama GT, Edirisinghe P, Bolton JL, Thatcher GR, Bioconjug Chem. 2009 Apr;20(4):728-41. "Comparative methods for analysis of protein covalent modification by electrophilic quinoids formed from xenobiotics."  PMID: 19301905
  63. Volchenboum SL, Kristhansdottir K, Wolfgeher D, Kron SJ., Mol Cell Proteomics. 2009 May 11. [Epub ahead of print] "Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns." PMID: 19435713
  64. Manolopoulou M, Guo Q, Malito E, Schilling AB, Tang WJ., J Biol Chem. 2009 Mar 25. [Epub ahead of print] "Molecular basis of catalytic chamber assisted unfolding and cleavage of human insulin by human insulin degrading enzyme."
  65. Xu H, Freitas MA, Bioinformatics. 2009 May 15;25(10):1341-3. "Automated Diagnosis of LC-MS/MS Performance." PMID: 19304874
  66. Li Q, Roxas BA, BMC Bioinformatics. 2009 Feb 2;10:43. "An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters."
  67. Ye H, Wang A, Lee BS, Yu T, Sheng S, Peng T, Hu S, Crowe DL, Zhou X. "Proteomic based identification of manganese superoxide dismutase 2 (SOD2) as a metastasis marker for oral squamous cell carcinoma." Cancer Genomics Proteomics. 2008 Mar-Apr;5(2):85-94. PMID: 18460737
  68. Lee BS, Lasanthi GD, Jayathilaka P, Huang JS, Gupta S., J Biomol Tech. 2008 Apr;19(2):106-8. "Immobilized metal affinity electrophoresis: a novel method of capturing phosphoproteins by electrophoresis."
  69. Qin Z, Kastrati I, Ashgodom RT, Lantvit DD, Overk CR, Choi Y, van Breemen RB, Bolton JL, Thatcher GR., Drug Metab Dispos. 2009 Jan;37(1):161-9. Epub 2008 Oct 20 "Structural modulation of oxidative metabolism in design of improved benzothiophene selective estrogen receptor modulators."
  70. Doan N, Gettins PG., J Biol Chem. 2008 Oct 17;283(42):28747-56. Epub 2008 Aug 12. "alpha-Macroglobulins are present in some gram-negative bacteria: characterization of the alpha2-macroglobulin from Escherichia coli."
  71. Dietz BM, Liu D, Hagos GK, Yao P, Schinkovitz A, Pro SM, Deng S, Farnsworth NR, Pauli GF, van Breemen RB, Bolton JL. Chem Res Toxicol. 2008 Oct;21(10):1939-48. Epub 2008 Sep 23. "Angelica sinensis and its alkylphthalides induce the detoxification enzyme NAD(P)H: quinone oxidoreductase 1 by alkylating Keap1."
  72. Guo J, Liu A, Cao H, Luo Y, Pezzuto JM, van Breemen RB., Drug Metab Dispos. 2008 Oct;36(10):2104-12. Epub 2008 Jul 24. "Biotransformation of the chemopreventive agent 2',4',4-trihydroxychalcone (isoliquiritigenin) by UDP-glucuronosyltransferases."
  73. Westerheide SD, Anckar J, Stevens SM Jr, Sistonen L, Morimoto RI, Science. 2009 Feb 20;323(5917):1063-6. "Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1" PMID: 19229036
  74. Rao PK and Li Q, Jan 15 (2009) J Proteomics Bioinform 2: 019-031. doi:10.4172/jpb.1000058, "Principal Component Analysis of Proteome Dynamics in Iron-Starved Mycobacterium Tuberculosis." PMID: 19436767 [PubMed]
  75. Kristjansdottir K, Wolfgeher D, Lucius N, Angulo DS, Kron SJ. J Proteome Res. 2008 Jul;7(7):2812-24. "Phosphoprotein profiling by PA-GeLC-MS/MS." PMID: 18510356
  76. 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. Epub 2008 Aug 28. PMID: 18757373
  77. Rao, Prahlad; Rodriguez, G; Smith, Issar; Li, Qingbo, "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. PMID: 18690695
  78. J. Zhao, S.M. Camp, E.T. Chiang, A.B. Schilling, S.M. Dudek, and J.G.N. Garcia, "Identification of a novel protein kinase A-mediated phosphorylation sites on non-muscle myosin light chain kinase: nano-LC/MS/MS mass spectrometry methodology." Journal of Organ Dysfunction, 2008, submitted.
  79. Xu H, Wang L, Sallans L, Freitas MA, Proteomics. 2009 Apr;9(7):1763-70, "A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra."  PMID: 19288523
  80. Xu H, Freitas MA, Proteomics. 2009 Mar;9(6):1548-55, "MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data."  PMID: 19235167
  81. 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)
  82. 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)
  83. 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)
  84. 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)
  85. 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)
  86. 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)
  87. Morimoto RI. Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging. Genes Dev. 2008 Jun 1;22(11):1427-38. Review. (PubMed)
  88. 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)
  89. 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)
  90. 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)
  91. 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)
  92. 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)
  93. Lu SJ, Feng Q, Park JS, Vida L, Lee BS, Strausbauch M, Wettstein PJ, Honig GR, Lanza R. "Biologic properties and enucleation of red blood cells from human embryonic stem cells." Blood. 2008 Dec 1;112(12):4475-84. Epub 2008 Aug 19. PMID: 18713948
  94. Yuan C, Solaro RJ. Myofilament proteins: From cardiac disorders to proteomic changes. 2008. Proteomics Clin Appl 2: 788-799. (InterScience)
  95. 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)
  96. 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)
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Proteomics Services were established by a grant from The Searle Funds at the Chicago Community Trust to the Chicago Biomedical Consortium (CBC website).

For more information about Proteomics Services at the Mass spectrometry, Metabolomics and Proteomics Facility, email proteomics at uic.edu.
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