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. Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. Walls AC, Xiong X, Park YJ, Tortorici MA, Snijder J, Quispe J, Cameroni E, Gopal R, Dai M, Lanzavecchia A, Zambon M, Rey FA, Corti D, Veesler D. Cell. 2019 Feb 21;176(5):1026-1039.e15. doi: 10.1016/j.cell.2018.12.028. Epub 2019 Jan 31. link
  2. Pacific geoduck (Panopea generosa) resilience to natural pH variation. Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB. Comp Biochem Physiol Part D Genomics Proteomics. 2019 Jan 24;30:91-101. doi: 10.1016/j.cbd.2019.01.010. [Epub ahead of print] link
  3. Tools for 3D Interactome Visualization. Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE. J Proteome Res. 2018 Dec 18. doi: 10.1021/acs.jproteome.8b00703. [Epub ahead of print] link
  4. A tandem mass spectrometry sequence database search method for identification of O-fucosylated proteins by mass spectrometry. Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather ND, Deutsch EW, Kappe SHI, Moritz RL. J Proteome Res. 2018 Dec 7. doi: 10.1021/acs.jproteome.8b00638. [Epub ahead of print] link
  5. Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. Borst AJ, Weidle CE, Gray MD, Frenz B, Snijder J, Joyce MG, Georgiev IS, Stewart-Jones GB, Kwong PD, McGuire AT, DiMaio F, Stamatatos L, Pancera M, Veesler D. Elife. 2018 Nov 7;7. pii: e37688. doi: 10.7554/eLife.37688. [Epub ahead of print] link
  6. Urine Complement Proteins and the Risk of Kidney Disease Progression and Mortality in Type 2 Diabetes. Vaisar T, Durbin-Johnson B, Whitlock K, Babenko I, Mehrotra R, Rocke DM, Afkarian M. Diabetes Care. 2018 Nov;41(11):2361-2369. doi: 10.2337/dc18-0699. Epub 2018 Aug 27. link
  7. Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins. Ting SY, Bosch DE, Mangiameli SM, Radey MC, Huang S, Park YJ, Kelly KA, Filip SK, Goo YA, Eng JK, Allaire M, Veesler D, Wiggins PA, Peterson SB, Mougous JD. Cell. 2018 Oct 8. pii: S0092-8674(18)31249-2. doi: 10.1016/j.cell.2018.09.037. [Epub ahead of print] link
  8. Sex steroids mediate discrete effects on HDL cholesterol efflux capacity and particle concentration in healthy men. Rubinow KB, Vaisar T, Chao JH, Heinecke JW, Page ST. J Clin Lipidol. . 2018 Jul - Aug;12(4):1072-1082. doi: 10.1016/j.jacl.2018.04.013. Epub 2018 Apr 30. link
  9. MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides. Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL. Sci Rep.. 2018 Jun 18;8(1):9276. doi: 10.1038/s41598-018-27650-4. link
  10. Obesity and Insulin Resistance Promote Atherosclerosis through an IFNγ-Regulated Macrophage Protein Network. Reardon CA, Lingaraju A, Schoenfelt KQ, Zhou G, Cui C, Jacobs-El H, Babenko I, Hoofnagle A, Czyz D, Shuman H, Vaisar T, Becker L. Cell Rep.. 2018 Jun 5;23(10):3021-3030. doi: 10.1016/j.celrep.2018.05.010. link
  11. Mango: A general tool for CID-cleavable cross-linked peptide identification. Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Anal Chem. 2018 Apr 20. doi: 10.1021/acs.analchem.7b04991. [Epub ahead of print] link
  12. An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus. Snijder J, Ortego MS, Weidle C, Stuart AB, Gray MD, McElrath MJ, Pancera M, Veesler D, McGuire AT. Immunity. 2018 Apr 17;48(4):799-811.e9. doi: 10.1016/j.immuni.2018.03.026. link
  13. ALPK2 Promotes Cardiogenesis in Zebrafish and Human Pluripotent Stem Cells Hofsteen P, Robitaille AM, Strash N, Palpant N, Moon RT, Pabon L, Murray Ce. iScience 2018 Apr 27;(2)88-100. doi: 10.1016/j.isci.2018.03.010
  14. 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. 2018 Mar 1;34(5):795-802. doi: 10.1093/bioinformatics/btx601. link
  15. Panorama Public: A public repository for quantitative data sets processed in Skyline Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B. Mol Cell Proteomics. 2018 Feb 27. pii: mcp.RA117.000543. doi: 10.1074/mcp.RA117.000543 link
  16. Type 2 diabetes is associated with loss of HDL endothelium protective functions. Vaisar T, Couzens E, Hwang A, Russell M, Barlow CE, DeFina LF, Hoofnagle AN, Kim F. PLoS One. 2018 Mar 15;13(3):e0192616. doi: 10.1371 link
  17. 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. 2018 Mar 1;34(5):795-802. doi: 10.1093/bioinformatics/btx601. link
  18. Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome. Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S. J Proteomics . 2018 Feb 20;173:89-98. doi: 10.1016/j.jprot.2017.11.025. Epub 2017 Dec 5. link
  19. Sestd1 Encodes a Developmentally Dynamic Synapse Protein That Complexes With BCR Rac1-GAP to Regulate Forebrain Dendrite, Spine and Synapse Formation. Yang XY, Stanley RE, Ross AP, Robitaille AM, Gray JA, Cheyette BNR. Cereb Cortex. 2018 Feb 21. doi: 10.1093/cercor/bhy026. link
  20. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE. Cell Syst . 2018 Jan 24;6(1):136-141.e5. doi: 10.1016/j.cels.2017.10.017. Epub 2017 Nov 29. link
  21. Quantifying HDL proteins by mass spectrometry: how many proteins are there and what are their functions? Shao B, Heinecke JW. Expert Rev Proteomics. . 2018 Jan;15(1):31-40. doi: 10.1080/14789450.2018.1402680. Epub 2017 Nov 13. link
  22. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL. Proteomes. . 2017 Dec 27;6(1). pii: E2. doi: 10.3390/proteomes6010002. link
  23. Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections. Xiong X, Tortorici MA, Snijder J, Yoshioka C, Walls AC, Li W, McGuire AT, Rey FA, Bosch BJ, Veesler D. J Virol. . 2017 Nov 1. pii: JVI.01628-17. doi: 10.1128/JVI.01628-17. link
  24. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Walls AC, Tortorici MA, Snijder J, Xiong X, Bosch BJ, Rey FA, Veesler D. Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11157-11162. doi: 10.1073/pnas.1708727114. Epub 2017 Oct 3. link
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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 Oct 13;91(21). pii: e01005-17. doi: 10.1128/JVI.01005-17. Print 2017 Nov 1 link
  30. 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 Oct;24(10):1730-1738. doi: 10.1038/cdd.2017.101. Epub 2017 Jun 23. link
  31. 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 Sep;11(9-10). doi: 10.1002/prca.201700064. Epub 2017 Jul 10. link
  32. 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
  33. Long-lived pancreatic ductal adenocarcinoma slice cultures enable precise study of the immune microenvironment. Jiang X, Seo YD, Chang JH, Coveler A, Nigjeh EN, Pan S, Jalikis F, Yeung RS, Crispe IN, Pillarisetty VG. Oncoimmunology. 2017 May 25;6(7):e1333210. doi: 10.1080/2162402X.2017.1333210. eCollection 2017. link
  34. 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 Sep 15;241:42-52. doi: 10.1016/j.virusres.2017.05.005. Epub 2017 May 11. link
  35. 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 Jul;11(7-8). doi: 10.1002/prca.201700045. Epub 2017 Apr 19. link
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Chavez JD, Schweppe DK, Eng JK, Bruce JE. Cell Chem Biol. 2016 Jun 23. link
  52. 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 May 6;15(5):1725-31. doi: 10.1021/acs.jproteome.6b00014. Epub 2016 Apr 28. link
  53. 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
  54. 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. 2016 Feb;57(2):246-57. doi: 10.1194/jlr.M063701. Epub 2015 Dec 15. link
  55. 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
  56. 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
  57. 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
  58. 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
  59. 2015
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
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