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.

  1. 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 Feb 26. [Epub ahead of print] link
  2. 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 Feb 28. [Epub ahead of print] link
  3. 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 Mar 5. [Epub ahead of print] link
  4. Protein interactions, Posttranslational Modifications and Topologies in Human Cells. Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE. Mol Cell Proteomics. 2013 Jan 25. [Epub ahead of print] link
  5. 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 Jan 24. [Epub ahead of print] link
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification. Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE. J Proteome Res. 2012 Mar 2;11(3):1621-32. Epub 2012 Feb 21. link
  25. 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
  26. 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
  27. 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
  28. Rapid empirical discovery of optimal peptides for targeted proteomics. Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, Maccoss MJ. Nat Methods. 2011 Nov 6;8(12):1041-3. doi: 10.1038/nmeth.1770. link
  29. 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
  30. A face in the crowd: recognizing peptides through database search. Eng JK, Searle BC, Clauser KR, Tabb DL. Mol Cell Proteomics. 2011 Nov;10(11):R111.009522. Epub 2011 Aug 29. link
  31. 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
  32. 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
  33. 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
  34. New structural proteins of Halobacterium salinarum gas vesicle revealed by comparative proteomics analysis. Chu LJ, Chen MC, Setter J, Tsai YS, Yang H, Fang X, Ting YS, Shaffer SA, Taylor GK, von Haller PD, Goodlett DR, Ng WV. J Proteome Res. 2011 Mar 4;10(3):1170-8. Epub 2011 Jan 25. link
  35. 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
  36. 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
  37. 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
  38. Sequence assignment of ADP-ribosylated peptides is facilitated as peptide length increases. Hengel SM, Icenogle L, Collins C, Goodlett DR. Commun Mass Spectrom. 2010 Aug 15;24(15):2312-6. link
  39. 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
  40. 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
  41. A review of tandem mass spectrometry characterization of adenosine diphosphate-ribosylated peptides. Hengel SM, Goodlett DR. Int J Mass Spectrome. doi:10.1016/j.ijms.2011.06.003. Available online 12 June 2011. link
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. Dipole-guided electron capture causes abnormal dissociations of phosphorylated pentapeptides. Moss CL, Chung TW, Wyer JA, Nielsen SB, Hvelplund P, Turecek F. J Am Soc Mass Spectrom. 2011 Apr;22(4):731-51. Epub 2011 Feb 26. link
  48. 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
  49. 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
  50. 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
  51. COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ. Proteomics. 2011 Mar;11(6):1064-74. doi: 10.1002/pmic.201000616. Epub 2011 Feb 7. link
  52. New structural proteins of Halobacterium salinarum gas vesicle revealed by comparative proteomics analysis. Chu LJ, Chen MC, Setter J, Tsai YS, Yang H, Fang X, Ting YS, Shaffer SA, Taylor GK, von Haller PD, Goodlett DR, Ng WV. J Proteome Res. 2011 Mar 4;10(3):1170-8. Epub 2011 Jan 25. link
  53. Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics. Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Turecek F. J Am Soc Mass Spectrom. 2011 Jan;22(1):13-30. Epub 2011 Jan 20. link
  54. Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ. Anal Chem. 2010 Dec 15;82(24):10116-24. Epub 2010 Nov 19. link
  55. Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology. Hoopmann MR, Weisbrod CR, Bruce JE. J Proteome Res. 2010 Dec 3;9(12):6323-33. Epub 2010 Nov 10. link
  56. 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
  57. Precursor charge state prediction for electron transfer dissociation tandem mass spectra. Sharma V, Eng JK, Feldman S, von Haller PD, Maccoss MJ, Noble WS. J Proteome Res. 2010 Oct 1;9(10):5438-44. link
  58. 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
  59. 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
  60. Comprehensive structure characterization of lipid A extracted from Yersinia pestis for determination of its phosphorylation configuration. Jones JW, Cohen IE, Turecek F, Goodlett DR, Ernst RK. J Am Soc Mass Spectrom. 2010 May;21(5):785-99. Epub 2010 Jan 25. link
  61. 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
  62. 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. 2010 Apr 13;4(1):61-71. link
  63. Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation datasets. Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R. Proteomics. 2010 Mar;10(6):1190-5. link
  64. Proteomics data repositories. Riffle M, Eng JK. Proteomics. 2009 Oct;9(20):4653-63. link
  65. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR. Anal Chem. 2009 Aug 1;81(15):6481-8. link
  66. Control of promatrilysin (MMP7) activation and substrate-specific activity by sulfated glycosaminoglycans. Ra HJ, Harju-Baker S, Zhang F, Linhardt RJ, Wilson CL, Parks WC. J Biol Chem. 2009 Oct 9;284(41):27924-32. Epub 2009 Aug 4. link
  67. Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures. Hoopmann MR, Merrihew GE, von Haller PD, Maccoss MJ. J Proteome Res. 2009 Apr;8(4):1870-5. link
  68. New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. Major MB, Roberts BS, Berndt JD, Marine S, Anastas J, Chung N, Ferrer M, Yi X, Stoick-Cooper CL, von Haller PD, Kategaya L, Chien A, Angers S, MacCoss M, Cleary MA, Arthur WT, Moon RT. Sci Signal. 2008 Nov 11;1(45):ra12. link
  69. Tandem Mass Spectrometry Investigation of ADP-ribosylated Kemptide. Hengel SM, Shaffer SA, Nunn BL, Goodlett DR. J Am Soc Mass Spectrom. 2009 Mar;20(3):477-83. Epub 2008 Nov 17. link
  70. Determination of pyrophosphorylated forms of lipid A in Gram-negative bacteria using a multivaried mass spectrometric approach. Jones JW, Shaffer SA, Ernst RK, Goodlett DR, Turecek F. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12742-7. Epub 2008 Aug 27. link
  71. A fast SEQUEST cross correlation algorithm. Eng JK, Fischer B, Grossmann J, Maccoss MJ. J Proteome Res. 2008 Oct;7(10):4598-602. Epub 2008 Sep 6. link
  72. MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M. Mol Cell Proteomics. 2008 Nov;7(11):2270-8. Epub 2008 Jul 18. link