Support for the publications involves either instrument access, computational analysis, consultation with lab or computational staff, etc. It is our policy that key collaborator(s) within the UWPR share in co-authorship of any manuscripts that are the result of work performed at the Resource. Minimally, the Proteomics Resource should always be acknowledged as follows in publications: This work is supported in part by the University of Washington's Proteomics Resource (UWPR95794).


  1. A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A. Anal Chem. 2024 May 2. doi: 10.1021/acs.analchem.4c00829. Online ahead of print. link
  2. Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod. Timmins-Schiffman E, Maas AE, Khanna R, Blanco-Bercial L, Huang E, Nunn BL. J Proteome Res. 2024 May 1. doi: 10.1021/acs.jproteome.4c00086. Online ahead of print. link
  3. A targeted proteomics method for quantifying plasma apolipoprotein kinetics in individual mice using stable isotope labeling. Shao B, Shimizu-Albergine M, Kramer F, Kanter JE, Heinecke JW, Vaisar T, Mittendorfer B, Patterson BW, Bornfeldt KE. J Lipid Res. 2024 Apr;65(4):100531. doi: 10.1016/j.jlr.2024.100531. Epub 2024 Mar 13. link
  4. Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod. Maas AE, Timmins-Schiffman E, Tarrant AM, Nunn BL, Park J, Blanco-Bercial L. Mol Ecol. 2024 Mar;33(6):e17284. doi: 10.1111/mec.17284. Epub 2024 Jan 22 link
  5. Flipped C-Terminal Ends of APOA1 Promote ABCA1-Dependent Cholesterol Efflux by Small HDLs. He Y, Pavanello C, Hutchins PM, Tang C, Pourmousa M, Vaisar T, Song HD, Pastor RW, Remaley AT, Goldberg IJ, Costacou T, Sean Davidson W, Bornfeldt KE, Calabresi L, Segrest JP, Heinecke JW. Circulation. 2024 Mar 5;149(10):774-787. doi: 10.1161/CIRCULATIONAHA.123.065959. Epub 2023 Nov 29. link
  6. Epigenetic programming of host lipid metabolism associates with resistance to TST/IGRA conversion after exposure to Mycobacterium tuberculosis. Dill-McFarland KA, Simmons JD, Peterson GJ, Nguyen FK, Campo M, Benchek P, Stein CM, Vaisar T, Mayanja-Kizza H, Boom WH, Hawn TR. bioRxiv [Preprint]. 2024 Mar 4:2024.02.27.582348. doi: 10.1101/2024.02.27.582348. link
  7. Sex differences in the associations of HDL particle concentration and cholesterol efflux capacity with incident coronary artery disease in type 1 diabetes: The RETRO HDLc cohort study. Costacou T, Miller RG, Bornfeldt KE, Heinecke JW, Orchard TJ, Vaisar T. J Clin Lipidol. 2024 Mar-Apr;18(2):e218-e229. doi: 10.1016/j.jacl.2024.01.004. Epub 2024 Jan 29. link
  8. A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes. Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. Lab Invest. 2024 Jan;104(1):100282. doi: 10.1016/j.labinv.2023.100282. Epub 2023 Nov 3. link


  9. An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting. Hodge, E.A., Chatterjee, A., Chen, C. et al. npj Viruses. 05 October 2023. link
  10. Subcellular proteomics for determining iron-limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta). Gomes KM, Nunn BL, Chappell PD, Jenkins BD. J Phycol. 2023 Oct;59(5):1085-1099. doi: 10.1111/jpy.13379. Epub 2023 Aug 24. link
  11. BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation. Witus SR, Tuttle LM, Li W, Zelter A, Wang M, Kermoade KE, Wilburn DB, Davis TN, Brzovic PS, Zhao W, Klevit RE. EMBO J. 2023 Aug 1;42(15):e113565. doi: 10.15252/embj.2023113565. Epub 2023 Jun 12. link
  12. BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation. Witus SR, Tuttle LM, Li W, Zelter A, Wang M, Kermoade KE, Wilburn DB, Davis TN, Brzovic PS, Zhao W, Klevit RE. EMBO J. 2023 Jun 12:e113565. doi: 10.15252/embj.2023113565. Online ahead of print. link
  13. hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics. Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK. ACS Infect Dis. 2023 Jun 9;9(6):1180-1189. doi: 10.1021/acsinfecdis.3c00010. Epub 2023 May 11. link
  14. Apolipoprotein C3 induces inflammasome activation only in its delipidated form. Hsu CC, Shao B, Kanter JE, He Y, Vaisar T, Witztum JL, Snell-Bergeon J, McInnes G, Bruse S, Gottesman O, Mullick AE, Bornfeldt KE. Nat Immunol. 2023 Mar;24(3):408-411. doi: 10.1038/s41590-023-01423-2. Epub 2023 Feb 13. link
  15. MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes. Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. bioRxiv [Preprint]. 2023 Mar 20:2023.03.16.533031. doi: 10.1101/2023.03.16.533031. link
  16. Disordered region encodes α-crystallin chaperone activity toward lens client γD-crystallin. Woods CN, Ulmer LD, Guttman M, Bush MF, Klevit RE. Proc Natl Acad Sci U S A. 2023 Feb 7;120(6):e2213765120. doi: 10.1073/pnas.2213765120. Epub 2023 Jan 31. link
  17. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL. J Proteome Res. 2023 Feb 3;22(2):615-624. doi: 10.1021/acs.jproteome.2c00624. Epub 2023 Jan 17. link
  18. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL. J Proteome Res. 2023 Feb 3;22(2):615-624. doi: 10.1021/acs.jproteome.2c00624. Epub 2023 Jan 17. link
  19. The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Kertesz-Farkas A, Nii Adoquaye Acquaye FL, Bhimani K, Eng JK, Fondrie WE, Grant C, Hoopmann MR, Lin A, Lu YY, Moritz RL, MacCoss MJ, Noble WS. J Proteome Res. 2023 Feb 3;22(2):561-569. doi: 10.1021/acs.jproteome.2c00615. Epub 2023 Jan 4. link


  20. Conditional Fragment Ion Probabilities Improve Database Searching for Nonmonoisotopic Precursors. O'Brien JJ, Gadzuk-Shea M, Seitzer PM, Rad R, McAllister FE, Schweppe DK. J Proteome Res. 2022 Nov 22. doi: 10.1021/acs.jproteome.2c00247. link
  21. Protein kinase R dependent phosphorylation of α-synuclein regulates its membrane binding and aggregation. Lasse Reimer, Hjalte Gram, Nanna Møller Jensen, Cristine Betzer, Li Yang, Lorrain Jin, Min Shi, Driss Boudeffa, Giuliana Fusco, Alfonso De Simone, Deniz Kirik, Hilal A Lashuel, Jing Zhang, Poul Henning Jensen PNAS Nexus. 2022 Nov; 1(5): pgac259. Published online 2022 Nov 16. doi: 10.1093/pnasnexus/pgac259. link
  22. The ProteomeXchange consortium at 10 years: 2023 update. Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Nucleic Acids Res.2022 Nov 12:gkac1040. doi: 10.1093/nar/gkac1040. link
  23. Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification. Smith IR, Eng JK, Barente AS, Hogrebe A, Llovet A, Rodriguez-Mias RA, Villén J. Anal Chem.2022 Nov 8;94(44):15198-15206. doi: 10.1021/acs.analchem.2c01711. Epub 2022 Oct 28. link
  24. Extracellular vesicles from gastric epithelial GES-1 cells infected with Helicobacter pylori promote changes in recipient cells associated with malignancy. González MF, Burgos-Ravanal R, Shao B, Heinecke J, Valenzuela-Valderrama M, Corvalán AH, Quest AFG Front Oncol. 2022 Oct 12;12:962920. doi: 10.3389/fonc.2022.962920. eCollection 2022. link
  25. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. Crandall G, Thompson RE, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts E. PeerJ2022 Oct 4. doi: 10.7717/peerj.14158 link
  26. Effect of Selective Androgen Receptor Modulator on Cholesterol Efflux Capacity, Size, and Subspecies of HDL Particles Guo W, Pencina KM, Furtado JD, Sacks FM, Vaisar T, Cheng M, Sniderman AD, Page ST, Bhasin S. J Endocr Soc. 2022 Jun 28;6(8):bvac099. doi: 10.1210/jendso/bvac099. eCollection 2022 Aug 1. link
  27. Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges. Boyd PW, Doney SC, EgginsS, Ellwood MH, Fourquez M, Nunn BL, Strzepek R, Timmins-Schiffman E. Limnology and Oceanography 25 June 2022. link
  28. Osmotic Processor for Enabling Sensitive and Rapid Biomarker Detection via Lateral Flow Assays. Chen SY, Wu AY, Lunde R, Lai JJ. Front Bioeng Biotechnol. 2022 Jun 1;10:884271. doi: 10.3389/fbioe.2022.884271. eCollection 2022. link
  29. 10,12-Conjugated linoleic acid supplementation improves HDL composition and function in mice. Vaisar T, Wang S, Omer M, Irwin AD, Storey C, Tang C, den Hartigh LJ. J Lipid Res. 2022 Jun 15;63(8):100241. doi: 10.1016/j.jlr.2022.100241. link
  30. Structural dynamics reveal isolate-specific differences at neutralization epitopes on HIV Env. Hodge EA, Naika GS, Kephart SM, Nguyen A, Zhu R, Benhaim MA, Guo W, Moore JP, Hu SL, Sanders RW, Lee KK. iScience. 2022 May 23;25(6):104449. doi: 10.1016/j.isci.2022.104449. eCollection 2022 Jun 17. link
  31. Conformational flexibility of apolipoprotein A-I amino- and carboxy-termini is necessary for lipid binding but not cholesterol efflux. Bedi S, Morris J, Shah A, Hart RC, Jerome WG, Aller SG, Tang C, Vaisar T, Bornfeldt KE, Segrest JP, Heinecke JW, Davidson WS. J Lipid Res. 2022 Mar;63(3):100168. doi: 10.1016/j.jlr.2022.100168. Epub 2022 Jan 17. link
  32. Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality. Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, Downing G, Chase D, Harvey EL, Whalen KE. mSphere 2021 May 12;6(3):e00009-21. doi: 10.1128/mSphere.00009-21. link
  33. Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load. Flores RL, Peterson ZE, Zelter A, Riffle M, Asbury CL, Davis TN. J Cell Biol. 2022 May 2;221(5):e202107016. doi: 10.1083/jcb.202107016. Epub 2022 Mar 30. link
  34. Pulmonary surfactant protein B carried by HDL predicts incident CVD in patients with type 1 diabetes. Shao B, Snell-Bergeon JK, Pyle LL, Thomas KE, de Boer IH, Kothari V, Segrest J, Davidson WS, Bornfeldt KE, Heinecke JW. J Lipid Res 2022 Apr;63(4):100196. doi: 10.1016/j.jlr.2022.100196. Epub 2022 Mar 14. link
  35. Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies. Sahoo A, Hodge EA, LaBranche CC, Styles TM, Shen X, Cheedarla N, Shiferaw A, Ozorowski G, Lee WH, Ward AB, Tomaras GD, Montefiori DC, Irvine DJ, Lee KK, Amara RR. Cell Rep. 2022 Mar 1;38(9):110436. doi: 10.1016/j.celrep.2022.110436. link
  36. Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry. Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A. Anal Chem. 2022 Mar 1;94(8):3501-3509. doi: 10.1021/acs.analchem.1c04101. Epub 2022 Feb 20. link
  37. Shotgun Proteomics Identifies Active Metabolic Pathways in Bleached Coral Tissue and Intraskeletal Compartments Axworthy, Jeremy B; Timmins-Schiffman, Emma; Brown, Tanya; Rodrigues, Lisa J; Nunn, Brook L. Frontiers in Marine Science. Lausanne (Feb 14, 2022). doi:10.3389/fmars.2022.797517. link
  38. Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice. Prasad VM, Leaman DP, Lovendahl KN, Croft JT, Benhaim MA, Hodge EA, Zwick MB, Lee KK. Cell 2022 Feb 4;185(4):641-653. dOI: link


  39. A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours Cui C, Chakraborty K, Tang XA, Schoenfelt KQ, Hoffman A, Blank A, McBeth B, Pulliam N, Reardon CA, Kulkarni SA, Vaisar T, Ballabio A, Krishnan Y, Becker L. Nat Nanotechnol. 2021 Dec;16(12):1394-1402. doi: 10.1038/s41565-021-00988-z. Epub 2021 Nov 11. link
  40. Amino acid primed mTOR activity is essential for heart regeneration. Miklas JW, Levy S, Hofsteen P, Mex DI, Clark E, Muster J, Robitaille AM, Sivaram G, Abell L, Goodson JM, Pranoto I, Madan A, Chin MT, Tian R, Murry CE, Moon RT, Wang Y, Ruohola-Baker H. iScience. 2021 Dec 6;25(1):103574. doi: 10.1016/j.isci.2021.103574. eCollection 2022 Jan 21. link
  41. Tandem Mass Spectrometry–Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing. Phipps WS, D Smith KD, Yang HY, Henderson CM, Pflaum H, Lerch ML, Fondrie WE, Emrick MA, Wu CC, MacCoss MJ, Noble WS, Hoofnagle AN. Am J of Clin Pathol. 2021 Nov 22; link
  42. CREBH normalizes dyslipidemia and halts atherosclerosis in diabetes by decreasing circulating remnant lipoproteins Shimizu-Albergine M, Basu D, Kanter JE, Kramer F, Kothari V, Barnhart S, Thornock C, Mullick AE, Clouet-Foraison N, Vaisar T, Heinecke JW, Hegele RA, Goldberg IJ, Bornfeldt KE. J Clin Invest. 2021 Nov 15;131(22):e153285. doi: 10.1172/JCI153285. link
  43. Altered HDL proteome predicts incident CVD in chronic kidney disease patients. Shao B, Mathew AV, Thornock C, Pennathur S; Michigan Kidney Translational Core CPROBE Investigator Group. J Lipid Res. 2021;62:100135. doi: 10.1016/j.jlr.2021.100135. Epub 2021 Oct 9. link
  44. Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora. Petrou K, Nunn BL, Padula MP, Miller DJ, Nielsen DA. Sci Rep. 2021 Sep 24;11(1):19061. doi: 10.1038/s41598-021-98548-x. link
  45. Decoding Post-Translational Modification Crosstalk With Proteomics. Leutert M, Entwisle SW, Villén J. Mol Cell Proteomics. 2021;20:100129. doi: 10.1016/j.mcpro.2021.100129. Epub 2021 Jul 30. link
  46. Apolipoprotein A-I modulates HDL particle size in the absence of apolipoprotein A-II Melchior JT, Street SE, Vaisar T, Hart R, Jerome J, Kuklenyik Z, Clouet-Foraison N, Thornock C, Bedi S, Shah AS, Segrest JP, Heinecke JW, Davidson WS. J Lipid Res. 2021;62:100099. doi: 10.1016/j.jlr.2021.100099. Epub 2021 Jul 27. link
  47. Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant. Lin A, Plubell DL, Keich U, Noble WS. J Proteome Res. 2021 Aug 6;20(8):4153-4164. doi: 10.1021/acs.jproteome.1c00483. Epub 2021 Jul 8. link
  48. Improving power while controlling the false discovery rate when only a subset of peptides are relevant. Andy Lin, Deanna L. Plubell, Uri Keich, William S. Noble J Proteome Res. 2021 Aug 6; 20(8): 4153–4164. Published online 2021 Jul 8. link
  49. Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments. Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ. Environ Microbiol. 2021 Aug;23(8):4646-4660. doi: 10.1111/1462-2920.15656. Epub 2021 Jul 13. link
  50. Niacin Increases Atherogenic Proteins in High-Density Lipoprotein of Statin-Treated Subjects Ronsein GE, Vaisar T, Davidson WS, Bornfeldt KE, Probstfield JL, O'Brien KD, Zhao XQ, Heinecke JW. Arterioscler Thromb Vasc Biol. 2021 Aug;41(8):2330-2341. doi: 10.1161/ATVBAHA.121.316278. Epub 2021 link
  51. Identification of phosphosites that alter protein thermal stability. Smith IR, Hess KN, Bakhtina AA, Valente AS, Rodríguez-Mias RA, Villén J. Nat Methods. 2021 Jul;18(7):760-762. doi: 10.1038/s41592-021-01178-4. Epub 2021 Jun 17. link
  52. Neutrophil elastase selectively kills cancer cells and attenuates tumorigenesis. Cui C, Chakraborty K, Tang XA, Zhou G, Schoenfelt KQ, Becker KM, Hoffman A, Chang YF, Blank A, Reardon CA, Kenny HA, Vaisar T, Lengyel E, Greene G, Becker L. Cell. 2021 Jun 10;184(12):3163-3177.e21. doi: 10.1016/j.cell.2021.04.016. Epub 2021 May 7. link
  53. Bacterial quorum-sensing signal arrests phytoplankton cell division and impacts virus-induced mortality. Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, Downing G, Chase D, Harvey EL, Whalen KE. mSphere. 2021 May 12;6(3):e00009-21. doi: 10.1128/mSphere.00009-21. link
  54. Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Timmins-Schiffman E, White SJ, Thompson RE, Vadopalas B, Eudeline B, Nunn BL, Roberts SB. Environ Microbiome. 2021 Mar 31;16(1):7. doi: 10.1186/s40793-021-00376-z. link
  55. Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Mudge MC, Nunn BL, Firth E, Ewert M, Hales K, Fondrie WE, Noble WS, Toner J, Light B, Junge KA. Environ Microbiol. 2021 Mar 24. doi: 10.1111/1462-2920.15485. link
  56. HCN Channel Phosphorylation Sites Mapped by Mass Spectrometry in Human Epilepsy Patients and in an Animal Model of Temporal Lobe Epilepsy. Concepcion FA, Khan MN, Ju Wang JD, Wei AD, Ojemann JG, Ko AL, Shi Y, Eng JK, Ramirez JM, Poolos NP. Neuroscience. 2021 Feb 9:S0306-4522(21)00063-4. doi: 10.1016/j.neuroscience.2021.01.038. link
  57. Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors. Tisthammer KH, Timmins-Schiffman E, Seneca FO, Nunn BL, Richmond RH. Sci Rep. 2021 Feb 9;11(1):3423. doi: 10.1038/s41598-021-82569-7. link


  58. Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2. Alexandra C Walls, Brooke Fiala, Alexandra Schäfer, Samuel Wrenn, Minh N Pham, Michael Murphy, Longping V Tse, Laila Shehata, Megan A O'Connor, Chengbo Chen, Mary Jane Navarro, Marcos C Miranda, Deleah Pettie, Rashmi Ravichandran, John C Kraft, Cassandra Ogohara, Anne Palser, Sara Chalk, E-Chiang Lee, Elizabeth Kepl, Cameron M Chow, Claire Sydeman, Edgar A Hodge, Brieann Brown, Jim T Fuller, Kenneth H Dinnon, Lisa E Gralinski, Sarah R Leist, Kendra L Gully, Thomas B Lewis, Miklos Guttman, Helen Y Chu, Kelly K Lee, Deborah H Fuller, Ralph S Baric, Paul Kellam, Lauren Carter, Marion Pepper, Timothy P Sheahan, David Veesler, Neil P King Cell 2020 Nov 25;183(5):1367-1382.e17. doi: 10.1016/j.cell.2020.10.043. Epub 2020 Oct 31. link
  59. Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc. Trigg SA, Mitchell KR, Thompson RE, Eudeline B, Vadopalas B, Timmins-Schiffman EB, Roberts SB. BMC Genomics 2020 Oct 19;21(1):723. doi: 10.1186/s12864-020-07127-3. link
  60. Diabetes Impairs Cellular Cholesterol Efflux from ABCA1 to Small HDL Particles. He Y, Ronsein GE, Tang C, Jarvik GP, Davidson WS, Kothari V, Song HD, Segrest J, Bornfeldt KE, Heinecke JW. Circ Res. 2020 Oct 9;127(9):1198-1210. doi: 10.1161/CIRCRESAHA.120.317178. Epub 2020 Aug 21. link
  61. Parallel Murine and Human Plaque Proteomics Reveals Pathways of Plaque Rupture. Vaisar T, Hu JH, Airhart N, Fox KA, Heinecke JW, Nicosia RF, Kohler TR, Potter ZE, Simon GM, Dix M, Cravatt B, Gharib SA, Dichek D. Circ Res. 2020 Sep 25;127(8):997-1022. doi: 10.1161/CIRCRESAHA.120.317295. Epub 2020 Jul 30. link
  62. Proteome and Phosphoproteome Analysis of Brown Adipocytes Reveals That RICTOR Loss Dampens Global Insulin/AKT Signaling. Entwisle SW, Martinez Calejman C, Valente AS, Lawrence RT, Hung CM, Guertin DA, Villén J. Mol Cell Proteomics. 2020 Jul;19(7):1104-1119. doi: 10.1074/mcp.RA120.001946. Epub 2020 Mar 31. link
  63. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. ACS Chem Biol. 2020 Jul 17;15(7):2005-2016. doi: 10.1021/acschembio.0c00429. Epub 2020 Jun 23. link
  64. Presence of serum amyloid A3 in mouse plasma is dependent on the nature and extent of the inflammatory stimulus. Chait A, den Hartigh LJ, Wang S, Goodspeed L, Babenko I, Altemeier WA, Vaisar T. Sci Rep 2020 Jun 25;10(1):10397. doi: 10.1038/s41598-020-66898-7. link
  65. Systemic Proteome Alterations Linked to Early Stage Pancreatic Cancer in Diabetic Patients. Peng H, Pan S, Yan Y, Brand RE, Petersen GM, Chari ST, Lai LA, Eng JK, Brentnall TA, Chen R. Cancers (Basel). 2020 Jun 11;12(6):1534. doi: 10.3390/cancers12061534. link
  66. Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP. J Proteome Res. 2020 May 1;19(5):2026-2034. doi: 10.1021/acs.jproteome.9b00860. Epub 2020 Apr 6. link
  67. Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format. Eng JK, Deutsch EW. Proteomics. 2020 Nov;20(21-22):e1900362. doi: 10.1002/pmic.201900362. Epub 2020 Apr 2. link
  68. Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates. Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB. Sci Rep. Apr 8;10(1):6042. doi: 10.1038/s41598-020-63218-x. link
  69. Increased Drp1 Acetylation by Lipid Overload Induces Cardiomyocyte Death and Heart Dysfunction. Hu Q, Zhang H, Gutiérrez Cortés N, Wu D, Wang P, Zhang J, Mattison JA, Smith E, Bettcher LF, Wang M, Lakatta EG, Sheu SS, Wang W. Circ Res. 2020 Feb 14;126(4):456-470. doi: 10.1161/CIRCRESAHA.119.315252. Epub 2020 Jan 3. link
  70. In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes. Zhong X, Wu X, Schweppe DK, Chavez JD, Mathay M, Eng JK, Keller A, Bruce JE. J Am Soc Mass Spectrom. 2020 Feb 5;31(2):190-195. doi: 10.1021/jasms.9b00021. Epub 2019 Nov 21. link
  71. A proteomic atlas of senescence-associated secretomes for aging biomarker development. Basisty N, Kale A, Jeon OH, Kuehnemann C, Payne T, Rao C, Holtz A, Shah S, Sharma V, Ferrucci L, Campisi J, Schilling B. PLoS Biol. 2020 Jan 16;18(1):e3000599. doi: 10.1371/journal.pbio.3000599. eCollection 2020 Jan. link
  72. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152. doi: 10.1093/nar/gkz984. link
  73. High Concentration of Medium-Sized HDL Particles and Enrichment in HDL Paraoxonase 1 Associate With Protection From Vascular Complications in People With Long-standing Type 1 Diabetes. Vaisar T, Kanter JE, Wimberger J, Irwin AD, Gauthier J, Wolfson E, Bahnam V, Wu IH, Shah H, Keenan HA, Greenbaum CJ, King GL, Heinecke JW, Bornfeldt KE. Diabetes Care 2020 Jan;43(1):178-186. doi: 10.2337/dc19-0772. Epub 2019 Oct 9. link


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  259. 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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  261. 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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  273. 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
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