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. ELISA reagent coverage evaluation by affinity purification tandem mass spectrometry. Henry SM, Sutlief E, Salas-Solano O, Valliere-Douglass J. MAbs. 2017 Oct;9(7):1065-1075. doi: 10.1080/19420862.2017.1349586. Epub 2017 Jul 14. link
  2. Sipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics. Guo X, Li Z, Yao Q, Mueller RS, Eng JK, Tabb DL, Hervey WJ 4th, Pan C. Bioinformatics. 2017 Sep 22. doi: 10.1093/bioinformatics/btx601. [Epub ahead of print] link
  3. First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H. Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10125-10130. doi: 10.1073/pnas.1706907114. Epub 2017 Sep 1. link
  4. Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation. Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB. J Proteome Res. 2017 Sep 1;16(9):3298-3309. doi: 10.1021/acs.jproteome.7b00288. Epub 2017 Aug 11. link
  5. Disrupting glutamine metabolic pathways to sensitize gemcitabine-resistant pancreatic cancer. Chen R, Lai LA, Sullivan Y, Wong M, Wang L, Riddell J, Jung L, Pillarisetty VG, Brentnall TA, Pan S. Sci Rep. 2017 Aug 11;7(1):7950. doi: 10.1038/s41598-017-08436-6. link
  6. Extracellular Matrix Proteins Mediate HIV-1 gp120 Interactions with α4β7. Plotnik D, Guo W, Cleveland B, von Haller P, Eng JK, Guttman M, Lee KK, Arthos J, Hu SL. J Virol. 2017 Aug 16. pii: JVI.01005-17. doi: 10.1128/JVI.01005-17. [Epub ahead of print] link
  7. Ageing and hypoxia cause protein aggregation in mitochondria. Kaufman DM, Wu X, Scott BA, Itani OA, Van Gilst MR, Bruce JE, Michael Crowder C. Cell Death Differ. 2017 Jun 23. doi: 10.1038/cdd.2017.101. [Epub ahead of print] link
  8. Spectral library-based glycopeptide analysis - detection of circulating galectin-3 binding protein in pancreatic cancer. Nigjeh EN, Chen R, Allen-Tamura Y, Brand RE, Brentnall TA, Pan S. Proteomics Clin Appl. 2017 Jun 19. doi: 10.1002/prca.201700064. [Epub ahead of print] link
  9. WNT/β-catenin signaling regulates mitochondrial activity to alter the oncogenic potential of melanoma in a PTEN-dependent manner. Brown K, Yang P, Salvador D, Kulikauskas R, Ruohola-Baker H, Robitaille AM, Chien AJ, Moon RT, Sherwood V. Oncogene. 2017 Jun 1;36(22):3119-3136. doi: 10.1038/onc.2016.450. Epub 2017 Jan 16. link
  10. Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry. Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Heck MC. Virus Res. 2017 May 11. pii: S0168-1702(16)30840-1. doi: 10.1016/j.virusres.2017.05.005. [Epub ahead of print] link
  11. An alpha-synuclein MRM assay with diagnostic potential for Parkinson's disease and monitoring disease progression. Yang L, Stewart T, Shi M, Pottiez G, Dator R, Wu R, Aro P, Schuster RJ, Ginghina C, Pan C, Gao Y, Qian W, Zabetian CP, Hu SC, Quinn JF, Zhang J. Proteomics Clin Appl. 2017 Mar 20. doi: 10.1002/prca.201700045. [Epub ahead of print] link
  12. Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. Sychev ZE, Hu A, DiMaio TA, Gitter A, Camp ND, Noble WS, Wolf-Yadlin A, Lagunoff M. PLoS Pathog. 2017 Mar 3;16(3):1228-1238. doi: 10.1021/acs.jproteome.6b00829. Epub 2017 Feb 7. link
  13. Mass-Spectrometry-Based Method To Quantify in Parallel Tau and Amyloid β 1-42 in CSF for the Diagnosis of Alzheimer's Disease. Pottiez G, Yang L, Stewart T, Song N, Aro P, Galasko DR, Quinn JF, Peskind ER, Shi M, Zhang J. J Proteome Res. 2017 Mar 3;13(3):e1006256. doi: 10.1371/journal.ppat.1006256. eCollection 2017 Mar. link
  14. 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. 2017 Feb;11(2):309-314. doi: 10.1038/ismej.2016.132. link
  15. Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers. Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE. J Proteome Res. 2017 Feb 3;16(2):720-727. doi: 10.1021/acs.jproteome.6b00752. link
  16. Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish. Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT. Proc Natl Acad Sci U S A 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114. link
  17. Proteome analysis of mast cell releasates reveals a role for chymase in the regulation of coagulation factor XIIIA levels via proteolytic degradation. Shubin NJ, Glukhova VA, Clauson M, Truong P, Abrink M, Pejler G, White NJ, Deutsch GH, Reeves SR, Vaisar T, James RG, Piliponsky AM. J Allergy Clin Immunol. 2017 Jan;139(1):323-334. doi: 10.1016/j.jaci.2016.03.051. link
  18. 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
  19. 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
  20. 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;11(12):e0167547. doi: 10.1371/journal.pone.0167547. link
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Chavez JD, Schweppe DK, Eng JK, Bruce JE. Cell Chem Biol. 2016 Jun 23. link
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 2015
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 2014
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 2013
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
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