UWPR Supported Publications

This work is supported in part by the University of Washington's Proteomics Resource (UWPR95794).

Here is a list of publications supported in part by the UWPR. Support for the publications involves either instrument access, computational analysis, consultation with lab or computational staff, etc.

    2017
  1. Quantitative Proteomics Based on Optimized Data-Independent Acquisition in Plasma Analysis. Nigjeh EN, Chen R, Brand RE, Petersen GM, Chari ST, von Haller PD, Eng JK, Feng Z, Yan Q, Brentnall TA, Pan S. J Proteome Res. 2017 Jan 3. link
  2. Tartrate-Resistant Acid Phosphatase Deficiency in the Predisposition to Systemic Lupus Erythematosus. An J, Briggs TA, Dumax-Vorzet A, Alarcón-Riquelme ME, Belot A, Beresford M, Bruce IN, Carvalho C, Chaperot L, Frostegård J, Plumas J, Rice GI, Vyse TJ, Wiedeman A, Crow YJ, Elkon KB. Arthritis Rheumatol. 2017 Jan;69(1):131-142. doi: 10.1002/art.39810. link
    2016
  3. A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. Chavez JD, Eng JK, Schweppe DK, Cilia M, Rivera K, Zhong X, Wu X, Allen T, Khurgel M, Kumar A, Lampropoulos A, Larsson M, Maity S, Morozov Y, Pathmasiri W, Perez-Neut M, Pineyro-Ruiz C, Polina E, Post S, Rider M, Tokmina-Roszyk D, Tyson K, Vieira Parrine Sant'Ana D, Bruce JE. PLoS One. 2016 Dec 20. link
  4. In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, Singh PK, Manoil C, Bruce JE. Nat Commun. 2016 Nov 11. link
  5. Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL. ISME J. 2016 Nov 8. doi: 10.1038/ismej.2016.132. [Epub ahead of print] link
  6. Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Walls AC, Tortorici MA, Frenz B, Snijder J, Li W, Rey FA, DiMaio F, Bosch BJ, Veesler D. Nat Struct Mol Biol. 2016 Oct;23(10):899-905. doi: 10.1038/nsmb.3293. link
  7. Wnt/β-catenin signaling promotes self-renewal and inhibits the primed state transition in naïve human embryonic stem cells. Xu Z, Robitaille AM, Berndt JD, Davidson KC, Fischer KA, Mathieu J, Potter JC, Ruohola-Baker H, Moon RT. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6382-E6390. link
  8. Identification of the nuclear localisation signal of O-GlcNAc transferase and its nuclear import regulation. Seo HG, Kim HB, Kang MJ, Ryum JH, Yi EC, Cho JW. Sci Rep. 2016 Oct 7. link
  9. XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data. Schweppe DK, Zheng C, Chavez JD, Navare AT, Wu X, Eng JK, Bruce JE. Bioinformatics. 2016 Sep 1. link
  10. ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. Riffle M, Jaschob D, Zelter A, Davis TN. J Proteome Res. 2016 Aug 5;15(8):2863-70. doi: 10.1021/acs.jproteome.6b00274.. link
  11. In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Chavez JD, Schweppe DK, Eng JK, Bruce JE. Cell Chem Biol. 2016 Jun 23. link
  12. Spectral library searching to identify crosslinked peptides. Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE. J Proteome Res. 2016 Apr 18. [Epub ahead of print] link
  13. Quantitative proteomics identify DAB2 as a cardiac developmental regulator that inhibits WNT/β-catenin signaling. Hofsteen P, Robitaille AM, Chapman DP, Moon RT, Murry CE. Proc Natl Acad Sci U S A. 2016 Jan 26;113(4):1002-7. doi: 10.1073/pnas.1523930113. Epub 2016 Jan 11. link
  14. Proteomic analysis of HDL from inbred mice strains implicates APOE associated with HDL in reduced cholesterol efflux capacity via the ABCA1 pathway. Pamir N, Hutchins P, Ronsein G, Vaisar T, Reardon CA, Getz GS, Lusis AJ, Heinecke JW. J Lipid Res. 2015 Dec 15. pii: jlr.M063701. [Epub ahead of print] link
  15. Targeted Proteomics Identifies Paraoxonase/Arylesterase 1 (PON1) and Apolipoprotein Cs as Potential Risk Factors for Hypoalphalipoproteinemia in Diabetic Subjects Treated with Fenofibrate and Rosiglitazone. Ronsein GE, Reyes-Soffer G, He Y, Oda M, Ginsberg H, Heinecke JW. Mol Cell Proteomics. 2016 Mar;15(3):1083-93. doi: 10.1074/mcp.M115.054528. Epub 2015 Dec 14. link
  16. Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology. DeBlasio SL, Chavez JD, Alexander MM, Ramsey J, Eng JK, Mahoney J, Gray SM, Bruce JE, Cilia M. J Virol. 2015 Dec 9;90(4):1973-87. doi: 10.1128/JVI.01706-15. link
  17. XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. Schweppe DK, Chavez JD, Bruce JE. Bioinformatics. 2016 Jan 15;32(2):306-8. doi: 10.1093/bioinformatics/btv519. link
  18. Serum amyloid A impairs the antiinflammatory properties of HDL. Han CY, Tang C, Guevara ME, Wei H, Wietecha T, Shao B, Subramanian S, Omer M, Wang S, O'Brien KD, Marcovina SM, Wight TN, Vaisar T, de Beer MC, de Beer FC, Osborne WR, Elkon KB, Chait A. J Clin Invest. 2016 Jan 4;126(1):266-81. doi: 10.1172/JCI83475. Epub 2015 Dec 7. link
  19. 2015
  20. The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H. Nat Cell Biol. 2015 Dec;17(12):1523-35. doi: 10.1038/ncb3264. Epub 2015 Nov 16. link
  21. Host-Microbe Protein Interactions during Bacterial Infection. Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE. Chem Biol. 2015 Nov 19 link
  22. Filamentous Bacteriophage Promote Biofilm Assembly and Function. Secor PR, Sweere JM, Michaels LA, Malkovskiy AV, Lazzareschi D, Katznelson E, Rajadas J, Birnbaum ME, Arrigoni A, Braun KR, Evanko SP, Stevens DA, Kaminsky W, Singh PK, Parks WC, Bollyky PL. Cell Host Microbe. 2015 Nov 11;18(5):549-59. doi: 10.1016/j.chom.2015.10.013. link
  23. A Quantitative Proteomic Analysis of Hemogenic Endothelium Reveals Differential Regulation of Hematopoiesis by SOX17. Clarke RL, Robitaille AM, Moon RT, Keller G. Stem Cell Reports. 2015 Aug 11;5(2):291-304. doi: 10.1016/j.stemcr.2015.07.008. link
  24. Quantitative interactome analysis reveals a chemoresistant edgotype. Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE. Nat Commun. 2015 Aug 3;6:7928. doi: 10.1038/ncomms8928. link
  25. Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Boyd PW, Dillingham PW, McGraw CM, Armstrong EA, Cornwall CE, Feng YY, Hurd CL, Gault-Ringold M, Roleda MY, Timmins-Schiffman E, Nunn BL Nat Climate Change 2015 Aug 27; doi:10.1038/nclimate2811. Epub 2015 Oct 5. link
  26. Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry. Sunhee Jung, Samuel A Danziger, Alexandre Panchaud, Priska von Haller, John D Aitchison, David R Goodlett J Proteomics Bioinform 2015; 8(10): 231–239. doi: 10.4172/jpb.1000374 link
  27. Site-specific activity of the acyltransferases HtrB1 and HtrB2 in Pseudomonas aeruginosa lipid A biosynthesis. Hittle LE, Powell DA, Jones JW, Tofigh M, Goodlett DR, Moskowitz SM, Ernst RK. Pathog Dis. 2015 Nov;73(8):ftv053. doi: 10.1093/femspd/ftv053. Epub 2015 Jul 29. link
  28. Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks. Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME. Mol Endocrinol. 2015 Aug;29(8):1195-218. doi: 10.1210/me.2015-1021. Epub 2015 Jul 16. link
  29. Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes. Palpant NJ, Pabon L, Roberts M, Hadland B, Jones D, Jones C, Moon RT, Ruzzo WL, Bernstein I, Zheng Y, Murry CE. Development. 2015 Sep 15;142(18):3198-209. doi: 10.1242/dev.117010. Epub 2015 Jul 7. link
  30. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development. Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ. J Am Soc Mass Spectrom. 2015 Nov;26(11):1827-36. doi: 10.1007/s13361-015-1193-z. Epub 2015 Jul 2. link
  31. A Deeper Look into Comet-Implementation and Features. Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. J Am Soc Mass Spectrom. 2015 Nov;26(11):1865-74. doi: 10.1007/s13361-015-1179-x. Epub 2015 Jun 27. link
  32. The Tec Kinase-Regulated Phosphoproteome Reveals a Mechanism for the Regulation of Inhibitory Signals in Murine Macrophages. Tampella G, Kerns HM, Niu D, Singh S, Khim S, Bosch KA, Garrett ME, Moguche A, Evans E, Browning B, Jahan TA, Nacht M, Wolf-Yadlin A, Plebani A, Hamerman JA, Rawlings DJ, James RG. J Immunol. 2015 Jul 1;195(1):246-56. doi: 10.4049/jimmunol.1403238. Epub 2015 May 29. link
  33. Dynamic proteome response of Pseudomonas aeruginosa to tobramycin antibiotic treatment. Wu X, Held K, Zheng C, Staudinger BJ, Chavez JD, Weisbrod CR, Eng JK, Singh PK, Manoil C, Bruce JE. Mol Cell Proteomics. 2015 Aug;14(8):2126-37. doi: 10.1074/mcp.M115.050161. Epub 2015 May 27. link
  34. A Cluster of Proteins Implicated in Kidney Disease Is Increased in High-Density Lipoprotein Isolated from Hemodialysis Subjects. Shao B, de Boer I, Tang C, Mayer PS, Zelnick L, Afkarian M, Heinecke JW, Himmelfarb J. J Proteome Res. 2015 Jul 2;14(7):2792-806. doi: 10.1021/acs.jproteome.5b00060. Epub 2015 Jun 15. link
  35. Inflammatory remodeling of the HDL proteome impairs cholesterol efflux capacity. Vaisar T, Tang C, Babenko I, Hutchins P, Wimberger J, Suffredini AF, Heinecke JW. J Lipid Res. 2015 Aug;56(8):1519-30. doi: 10.1194/jlr.M059089. Epub 2015 May 20. link
  36. Combining Near-UV Photodissociation with Electron Transfer. Reduction of the Diazirine Ring in a Photomethionine-Labeled Peptide Ion. Shaffer CJ, Marek A, Nguyen HT, Tureček F. J Am Soc Mass Spectrom. 2015 Aug;26(8):1367-81. doi: 10.1007/s13361-015-1139-5. Epub 2015 Apr 23. link
  37. Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. Jaschob D, Davis TN, Riffle M. BMC Res Notes. 2015 Mar 7;8:70. doi: 10.1186/s13104-015-1009-z. link
  38. Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry. Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE. Structure. 2015 Apr 7;23(4):762-73. doi: 10.1016/j.str.2015.01.022. Epub 2015 Mar 19. link
  39. Identification of synaptosomal proteins binding to monomeric and oligomeric α-synuclein. Betzer C, Movius AJ, Shi M, Gai WP, Zhang J, Jensen PH. PLoS One 2015 Feb 6;10(2):e0116473. doi: 10.1371/journal.pone.0116473. eCollection 2015. link
  40. Proteomic profiling in MPTP monkey model for early Parkinson disease biomarker discovery. Lin X, Shi M, Masilamoni JG, Dator R, Movius J, Aro P, Smith Y, Zhang J. Biochim Biophys Acta. 2015 Jul;1854(7):779-87. doi: 10.1016/j.bbapap.2015.01.007. Epub 2015 Jan 22. link
  41. Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. Shi M, Movius J, Dator R, Aro P, Zhao Y, Pan C, Lin X, Bammler TK, Stewart T, Zabetian CP, Peskind ER, Hu SC, Quinn JF, Galasko DR, Zhang J Mol Cell Proteomics 2015 Mar;14(3):544-55. doi: 10.1074/mcp.M114.040576. Epub 2015 Jan 2. link
  42. Suspended marine particulate proteins in coastal and oligotrophic waters. Bridoux MC, Neibauer J, Ingalls AE, Nunn BL, Keil RG. J Marine Systems 2015 Mar;143:39-48. doi:10.1016/j.jmarsys.2014.10.014 link
  43. Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics. Ronsein GE, Pamir N, von Haller PD, Kim DS, Oda MN, Jarvik GP, Vaisar T, Heinecke JW J Proteomics 2015 Jan 15;113:388-99. doi: 10.1016/j.jprot.2014.10.017. Epub 2014 Oct 31. link
  44. 2014
  45. An experimentally robust model of monomeric apolipoprotein A-I created from a chimera of two X-ray structures and molecular dynamics simulations. Segrest JP, Jones MK, Shao B, Heinecke JW. Biochemistry. 2014 Dec 9;53(48):7625-40. doi: 10.1021/bi501111j. Epub 2014 Nov 25. link
  46. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH, Roberts SB. BMC Genomics. 2014 Nov 3;15(1):951. link
  47. Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics. Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA. J Am Soc Mass Spectrom. 2014 Dec;25(12):2048-59. doi: 10.1007/s13361-014-0981-1. Epub 2014 Sep 27. link
  48. Crux: rapid open source protein tandem mass spectrometry analysis. McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS. J Proteome Res. 2014 Oct 3;13(10):4488-91. doi: 10.1021/pr500741y. Epub 2014 Sep 9. link
  49. Panorama: A Targeted Proteomics Knowledge Base. Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B. J Proteome Res. 2014 Sep 5;13(9):4205-10. doi: 10.1021/pr5006636. Epub 2014 Aug 18. link
  50. SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences. Jaschob D, Davis TN, Riffle M. BMC Res Notes. 2014 Jul 23;7:468. doi: 10.1186/1756-0500-7-468. link
  51. Plasma exosomal α-synuclein is likely CNS-derived and increased in Parkinson's disease. Shi M, Liu C, Cook TJ, Bullock KM, Zhao Y, Ginghina C, Li Y, Aro P, Dator R, He C, Hipp MJ, Zabetian CP, Peskind ER, Hu SC, Quinn JF, Galasko DR, Banks WA, Zhang J. Acta Neuropathol. 2014 Nov;128(5):639-50. doi: 10.1007/s00401-014-1314-y. Epub 2014 Jul 6. link
  52. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. Poulson-Ellestad KL, Jones CM, Roy J, Viant MR, Fernández FM, Kubanek J, Nunn BL. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):9009-14. doi: 10.1073/pnas.1402130111. Epub 2014 Jun 2. Erratum in: Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12568. link
  53. Targeted discovery and validation of plasma biomarkers of Parkinson's disease. Pan C, Zhou Y, Dator R, Ginghina C, Zhao Y, Movius J, Peskind E, Zabetian CP, Quinn J, Galasko D, Stewart T, Shi M, Zhang J. J Proteome Res. 2014 Nov 7;13(11):4535-45. Epub 2014 Jun 11. link
  54. Humans with atherosclerosis have impaired ABCA1 cholesterol efflux and enhanced high-density lipoprotein oxidation by myeloperoxidase. Shao B, Tang C, Sinha A, Mayer PS, Davenport GD, Brot N, Oda MN, Zhao XQ, Heinecke JW. Circ Res. 2014 May 23;114(11):1733-42. doi: 10.1161/CIRCRESAHA.114.303454. Epub 2014 Mar 19. link
  55. Collision-induced dissociation of diazirine-labeled peptide ions. Evidence for Brønsted-acid assisted elimination of nitrogen. Marek A, Tureček F. J Am Soc Mass Spectrom. 2014 May;25(5):778-89. doi: 10.1007/s13361-014-0832-0. Epub 2014 Feb 19. link
  56. Quantitative glycoproteomics analysis reveals changes in N-glycosylation level associated with pancreatic ductal adenocarcinoma. Pan S, Chen R, Tamura Y, Crispin DA, Lai LA, May DH, McIntosh MW, Goodlett DR, Brentnall TA. J Proteome Res. 2014 Mar 7;13(3):1293-306. doi: 10.1021/pr4010184. Epub 2014 Jan 28. link
  57. 2013
  58. Diatom proteomics reveals unique acclimation strategies to mitigate fe limitation. Nunn BL, Faux JF, Hippmann AA, Maldonado MT, Harvey HR, Goodlett DR, Boyd PW, Strzepek RF. PLoS One. 2013 Oct 16;8(10):e75653. doi: 10.1371/journal.pone.0075653. link
  59. Protein Kinase PKN1 represses Wnt/beta-catenin signaling in human melanoma cells. James RG, Bosch KA, Kulikauskas RM, Yang PT, Robin NC, Toroni RA, Biechele TL, Berndt JD, von Haller PD, Eng JK, Wolf-Yadlin A, Chien AJ, Moon RT. J Biol Chem. 2013 Nov 29;288(48):34658-70. doi: 10.1074/jbc.M113.500314. Epub 2013 Oct 10. link
  60. Electron transfer dissociation of photolabeled peptides. Backbone cleavages compete with diazirine ring rearrangements. Marek A, Pepin R, Peng B, Laszlo KJ, Bush MF, Turecek F. J Am Soc Mass Spectrom. 2013 Nov;24(11):1641-53. doi: 10.1007/s13361-013-0630-0. Epub 2013 Apr 30. link
  61. A disease-associated PTPN22 variant promotes systemic autoimmunity in murine models. Dai X, James RG, Habib T, Singh S, Jackson S, Khim S, Moon RT, Liggitt D, Wolf-Yadlin A, Buckner JH, Rawlings DJ. J Clin Invest. 2013 May 1;123(5):2024-36. doi: 10.1172/JCI66963. Epub 2013 Apr 24. link
  62. Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research. Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE. J Proteomics. 2013 Aug 2;88:109-19. doi: 10.1016/j.jprot.2013.04.009. Epub 2013 Apr 13. link
  63. Macrophage ADAM17 deficiency augments CD36-dependent apoptotic cell uptake and the linked anti-inflammatory phenotype. Driscoll WS, Vaisar T, Tang J, Wilson CL, Raines EW. Circ Res. 2013 Jun 21;113(1):52-61. doi: 10.1161/CIRCRESAHA.112.300683. Epub 2013 Apr 12. link
  64. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. Timmins-Schiffman EB Nunn BL, Goodlett DR and Roberts SB. Conservation Physiology. 2013 Apr 11; 1: doi:10.1093/conphys/cot009f link
  65. The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo. Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6400-5. doi: 10.1073/pnas.1221132110. Epub 2013 Mar 18. link
  66. Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry. Chapman JD, Gagné JP, Poirier GG, Goodlett DR. J Proteome Res. 2013 Apr 5;12(4):1868-80. doi: 10.1021/pr301219h. Epub 2013 Mar 18. link
  67. In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy. Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE. J Proteome Res. 2013 Apr 5;12(4):1569-79. doi: 10.1021/pr3011638. Epub 2013 Feb 28. link
  68. XLink-DB: Database and Software Tools for Storing and Visualizing Protein Interaction Topology Data. Zheng C, Weisbrod CR, Chavez JD, Eng JK, Sharma V, Wu X, Bruce JE. J Proteome Res. 2013 Apr 5;12(4):1989-95. doi: 10.1021/pr301162j. Epub 2013 Mar 5. link
  69. Protein interactions, Posttranslational Modifications and Topologies in Human Cells. Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE. Mol Cell Proteomics. 2013 May;12(5):1451-67. doi: 10.1074/mcp.M112.024497. Epub 2013 Jan 25. link
  70. Global analysis of condition-specific subcellular protein distribution and abundance. Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD. Mol Cell Proteomics. 2013 May;12(5):1421-35. doi: 10.1074/mcp.O112.019166. Epub 2013 Jan 24. link
  71. 2012
  72. Cross-linking mass spectrometry and mutagenesis confirm the functional importance of surface interactions between CYP3A4 and holo/apo cytochrome b(5). Zhao C, Gao Q, Roberts AG, Shaffer SA, Doneanu CE, Xue S, Goodlett DR, Nelson SD, Atkins WM. Biochemistry. 2012 Nov 27;51(47):9488-500. doi: 10.1021/bi301069r. Epub 2012 Nov 14. link
  73. Comet: an open source tandem mass spectrometry sequence database search tool. Eng JK, Jahan TA, Hoopmann MR. Proteomics. 2013 Jan;13(1):22-4. doi: 10.1002/pmic.201200439. Epub 2012 Dec 4. link
  74. De Novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics. Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, Maccoss MJ. J Am Soc Mass Spectrom. 2012 Dec;23(12):2075-82. doi: 10.1007/s13361-012-0482-z. Epub 2012 Sep 25. link
  75. An expansive human regulatory lexicon encoded in transcription factor footprints. Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. link
  76. Proteomic Classification of Acute Leukemias by Alignment-Based Quantitation of LC-MS/MS Data Sets. Foss EJ, Radulovic D, Stirewalt DL, Radich J, Sala-Torra O, Pogosova-Agadjanyan EL, Hengel SM, Loeb KR, Deeg HJ, Meshinchi S, Goodlett DR, Bedalov A. J Proteome Res. 2012 Oct 5;11(10):5005-10. doi: 10.1021/pr300567r. Epub 2012 Sep 11. link
  77. Perturbing peptide cation-radical electronic states by thioxoamide groups: formation, dissociations, and energetics of thioxopeptide cation-radicals. Zimnicka M1, Chung TW, Moss CL, Tureček F. J Phys Chem A. 2013 Feb 14;117(6):1265-75. doi: 10.1021/jp305865q. Epub 2012 Jul 20. link
  78. An Extraction Assay Analysis for Galanthamine in Guinea Pig Plasma and its Application to Nerve Agent Countermeasures Steiner WE, Pikalov IA, Williams PT, English WA, Hilmas CJ. J Anal Bioanal Techniques 2012, 3:5. doi: 10.4172/2155-9872.1000144. link
  79. Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides. Ledvina AR, Chung TW, Hui R, Coon JJ, Turecek F. J Am Soc Mass Spectrom. 2012 Aug;23(8):1351-63. Epub 2012 Jun 6. link
  80. Cascade dissociations of peptide cation-radicals. Part 1. Scope and effects of amino acid residues in penta-, nona-, and decapeptides. Chung TW, Hui R, Ledvina A, Coon JJ, Turecek F. J Am Soc Mass Spectrom. 2012 Aug;23(8):1336-50. Epub 2012 Jun 6. link
  81. Surface acoustic wave nebulization facilitating lipid mass spectrometric analysis. Yoon SH, Huang Y, Edgar JS, Ting YS, Heron SR, Kao Y, Li Y, Masselon CD, Ernst RK, Goodlett DR. Anal Chem. 2012 Aug 7;84(15):6530-7. link
  82. Chemical cross-linking, mass spectrometry and in silico modeling of proteasomal 20S core particles of the haloarchaeon Haloferax volcanii. Karadzic I, Maupin-Furlow J, Humbard M, Prunetti L, Singh P, Goodlett DR. Proteomics. 2012 Jun;12(11):1806-14. doi: 10.1002/pmic.201100260. link
  83. Development of a Novel LC/MS/MS Extraction Assay for Galanthamine in Guinea Pig Plasma and its Application to Nerve Agent Countermeasures. Steiner WE, Pikalov IA, Williams PT, English WA, Hilmas CJ Open Access Scientific Reports 2012. 1:149. doi:10.4172/scientificreports.149 link
  84. Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: protein synthesis, cell proliferation, and T-cell activation. Navare AT, Sova P, Purdy DE, Weiss JM, Wolf-Yadlin A, Korth MJ, Chang ST, Proll SC, Jahan TA, Krasnoselsky AL, Palermo RE, Katze MG. Virology. 2012 Jul 20;429(1):37-46. Epub 2012 Apr 26. link
  85. Surface acoustic wave nebulization produces ions with lower internal energy than electrospray ionization. Huang Y, Yoon SH, Heron SR, Masselon CD, Edgar JS, Turecek F, Goodlett DR. J Am Soc Mass Spectrom. 2012 Jun;23(6):1062-70. Epub 2012 Apr 3. link
  86. Cross-linking measurements of the otato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions. Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE. J Proteome Res. 2012 May 4;11(5):2968-81. Epub 2012 Mar 30. link
  87. Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. Pan S, Chen R, Brand RE, Hawley S, Tamura Y, Gafken PR, Milless BP, Goodlett DR, Rush J, Brentnall TA. J Proteome Res. 2012 Mar 2;11(3):1937-48. Epub 2012 Feb 8. link
  88. Multiple-Reaction Monitoring-Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures. Hoofnagle AN, Becker JO, Oda MN, Cavigiolio G, Mayer P, Vaisar T. Clin Chem. 2012 Apr;58(4):777-81. Epub 2012 Feb 3. link
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  90. Myeloperoxidase Targets Apolipoprotein A-I, the Major High Density Lipoprotein Protein, for Site-Specific Oxidation in Human Atherosclerotic Lesions. Shao B, Pennathur S, Heinecke JW. J Biol Chem. 2012 Feb 24. link
  91. In Vivo Application of Photocleavable Protein Interaction Reporter Technology. Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE. J Proteome Res. 2012 Feb 3;11(2):1027-41. Epub 2012 Jan 9. link
  92. MSDaPl (Mass Spectrometry Data Platform): A Proteomics Data Management Platform. Sharma V, Eng JK, Maccoss MJ, Riffle M. Mol Cell Proteomics. 2012 Sep;11(9):824-31. Epub 2012 May 18. link
  93. Sites of ubiquitin attachment in Saccharomyces cerevisiae. Starita LM, Lo RS, Eng JK, von Haller PD, Fields S. Proteomics. 2012 Jan;12(2):236-40. doi: 10.1002/pmic.201100166. Epub 2011 Dec 20 link
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  96. SILACtor: software to enable dynamic SILAC studies. Hoopmann MR, Chavez JD, Bruce JE. Anal Chem. 2011 Nov 15;83(22):8403-10. Epub 2011 Oct 27. link
  97. Tunable charge tags for electron-based methods of peptide sequencing: design and applications. Zimnicka M, Moss CL, Chung TW, Hui R, Tureček F. J Am Soc Mass Spectrom. 2012 Apr;23(4):608-20. doi: 10.1007/s13361-011-0184-y. Epub 2011 Jun 23. link
  98. Data-independent proteomic screen identifies novel tamoxifen agonist that mediates drug resistance. Hengel SM, Murray E, Langdon S, Hayward L, O'Donoghue J, Panchaud A, Hupp T, Goodlett DR. J Proteome Res. 2011 Oct 7;10(10):4567-78. Epub 2011 Sep 21. link
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  100. iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. Epub 2011 Aug 29. link
  101. The fasted/fed mouse metabolic acetylome: n6-acetylation differences suggest acetylation coordinates organ-specific fuel switching. Yang L, Vaitheesvaran B, Hartil K, Robinson AJ, Hoopmann MR, Eng JK, Kurland IJ, Bruce JE. J Proteome Res. 2011 Sep 2;10(9):4134-49. Epub 2011 Aug 16. link
  102. Cross-linking measurements of in vivo protein complex topologies. Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE. Mol Cell Proteomics. 2011 Oct;10(10):M110.006841. Epub 2011 Jun 22. link
  103. Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex. Helmlinger D, Marguerat S, Villen J, Swaney DL, Gygi SP, Bahler J, Winston F. EMBO J. 2011 Jun 3;30(14):2843-52. doi: 10.1038/emboj.2011.181. link
  104. Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells. Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE. PLoS One. 2011;6(5):e19892. Epub 2011 May 26. link
  105. Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses. Chu LJ, Yang H, Shih P, Kao Y, Tsai YS, Chen J, Huang G, Weng RR, Ting YS, Fang X, von Haller PD, Goodlett DR, Ng WV. J Proteome Res. 2011 Jul 1;10(7):3261-73. Epub 2011 Jun 14. link
  106. Fast parallel tandem mass spectral library searching using GPU hardware acceleration. Baumgardner LA, Shanmugam AK, Lam H, Eng JK, Martin DB. J Proteome Res. 2011 Jun 3;10(6):2882-8. Epub 2011 May 5. link
  107. Microdialysis combined with proteomics for protein identification in breast tumor microenvironment in vivo. Xu BJ, Yan W, Jovanovic B, Shaw AK, An QA, Eng J, Chytil A, Link AJ, Moses HL. Cancer Microenviron. 2011 Apr; 4(1): 61–71. Epub 2010 Apr 13. link
  108. Impact of HDL oxidation by the myeloperoxidase system on sterol efflux by the ABCA1 pathway. Shao B, Heinecke JW. J Proteomics. 2011 Oct 19;74(11):2289-99. Epub 2011 Apr 9. link
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  111. Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex. Gold MG, Stengel F, Nygren PJ, Weisbrod CR, Bruce JE, Robinson CV, Barford D, Scott JD. Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6426-31. Epub 2011 Apr 4. link
  112. Faster, quantitative, and accurate precursor acquisition independent from ion count. Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR. Anal Chem. 2011 Mar 15;83(6):2250-7. Epub 2011 Feb 22. link
  113. Proteomic analysis of acetaminophen-induced changes in mitochondrial protein expression using spectral counting. Stamper BD, Mohar I, Kavanagh TJ, Nelson SD. Chem Res Toxicol. 2011 Apr 18;24(4):549-58. Epub 2011 Feb 18. link
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  119. Urinary proteomics evaluation in interstitial cystitis/painful bladder syndrome: a pilot study. Goo YA, Tsai YS, Liu AY, Goodlett DR, Yang CC. Int Braz J Urol. 2010 Jul-Aug;36(4):464-78; discussion 478-9, 479. link
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  121. The histidine effect. Electron transfer and capture cause different dissociations and rearrangements of histidine peptide cation-radicals. Turecek F, Chung TW, Moss CL, Wyer JA, Ehlerding A, Holm AI, Zettergren H, Nielsen SB, Hvelplund P, Chamot-Rooke J, Bythell B, Paizs B. J Am Chem Soc. 2010 Aug 11;132(31):10728-40. link
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  123. CD90/THY1 is overexpressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker. True LD, Zhang H, Ye M, Huang CY, Nelson PS, von Haller PD, Tjoelker LW, Kim JS, Qian WJ, Smith RD, Ellis WJ, Liebeskind ES, Liu AY. Mod Pathol. 2010 Oct;23(10):1346-56. Epub 2010 Jun 18. link
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  125. Estimating false discovery rates for peptide and protein identification using randomized databases. Hather G, Higdon R, Bauman A, von Haller PD, Kolker E. Proteomics. 2010 Jun;10(12):2369-76. link
  126. A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies. Yang L, Tang X, Weisbrod CR, Munske GR, Eng JK, von Haller PD, Kaiser NK, Bruce JE. Anal Chem. 2010 May 1;82(9):3556-66. link
  127. Backbone and side-chain specific dissociations of z ions from non-tryptic peptides. Chung TW, Turecek F. J Am Soc Mass Spectrom. 2010 Aug;21(8):1279-95. Epub 2010 Feb 18. link
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