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).

2024

1. Detection and Quantification of Drug-Protein Adducts in Human Liver. Zelter A, Riffle M, Shteynberg DD, Zhong G, Riddle EB, Hoopmann MR, Jaschob D, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N.. J Proteome Res. 2024 Oct 23. doi: 10.1021/acs.jproteome.4c00663. Online ahead of print. link
2. Relationships between HDL subpopulation proteome and HDL function in overweight/obese people with and without coronary heart disease. Vaisar T, Babenko I, Horvath KV, Niisuke K, Asztalos BF. Atherosclerosis. 2024 Oct;397:118565. doi: 10.1016/j.atherosclerosis.2024.118565. Epub 2024 Aug 13. link
3. A Framework for Quality Control in Quantitative Proteomics. Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. J Proteome Res. 2024 Oct 4;23(10):4392-4408. doi: 10.1021/acs.jproteome.4c00363. Epub 2024 Sep 9. PMID: 39248652 link
4. 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 14;96(19):7373-7379. doi: 10.1021/acs.analchem.4c00829. Epub 2024 May 2. link
5. High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid. Ulmer LD, Canzani D, Woods CN, Stone NL, Janowska MK, Klevit RE, Bush MF. J Proteome Res. 2024 Aug 2;23(8):3560-3570. doi: 10.1021/acs.jproteome.4c00194. Epub 2024 Jul 5. link
6. Comparative Analysis of Protein Quantification by the SomaScan Assay versus Orthogonal Methods in Urine from People with Diabetic Kidney Disease. Lopez LN, Durbin-Johnson B, Vargas CR, Ruzinski J, Goodling A, Mehrotra R, Vaisar T, Rocke DM, Afkarian M. J Proteome Res. 2024 Jul 5;23(7):2598-2607. doi: 10.1021/acs.jproteome.4c00322. Epub 2024 Jun 18. link
7. 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
8. 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 Jun 7;23(6):2112-2123. doi: 10.1021/acs.jproteome.4c00086. Epub 2024 May 1.PMID: 38690632 link
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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

    2023

15. 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
16. 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
17. 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
18. 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
19. 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
20. 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
21. 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
22. 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
23. 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
24. 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

    2022

25. 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
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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. doi.org/10.1002/lno.12175 link
33. 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
34. 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
35. 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
36. 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
37. 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
38. 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
39. 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
40. 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
41. 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
42. 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
43. 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:https://doi.org/10.1016/j.cell.2022.01.013. link

    2021

44. 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
45. 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
46. 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; https://doi.org/10.1093/ajcp/aqab185. link
47. 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
48. 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
49. 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
50. 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
51. 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
52. 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
53. 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
54. 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
55. 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
56. 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
57. 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
58. 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
59. 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
60. 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
61. 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
62. 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

    2020

63. 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
64. 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
65. 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
66. 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
67. 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
68. 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
69. 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
70. 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
71. 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
72. 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
73. 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
74. 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
75. 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
76. 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
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78. 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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79. RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions. Schwerk J, Soveg FW, Ryan AP, Thomas KR, Hatfield LD, Ozarkar S, Forero A, Kell AM, Roby JA, So L, Hyde JL, Gale M Jr, Daugherty MD, Savan R. Nat Immunol. 2019 Dec;20(12):1610-1620. doi: 10.1038/s41590-019-0527-6. Epub 2019 Nov 18. link
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82. Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi. Krayushkina D, Timmins-Schiffman E, Faux J, May DH, Riffle M, Harvey HR, Nunn BL. Sci Data. 2019 Dec 3;6(1):303. doi: 10.1038/s41597-019-0308-y. link
83. Overcoming Steric Restrictions of VRC01 HIV-1 Neutralizing Antibodies through Immunization. Parks KR, MacCamy AJ, Trichka J, Gray M, Weidle C, Borst AJ, Khechaduri A, Takushi B, Agrawal P, Guenaga J, Wyatt RT, Coler R, Seaman M, LaBranche C, Montefiori DC, Veesler D, Pancera M, McGuire A, Stamatatos L. Cell Rep. 2019 Dec 3;29(10):3060-3072.e7. doi: 10.1016/j.celrep.2019.10.071. link
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90. Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL. ISME J. 2020 Jan;14(1):39-52. doi: 10.1038/s41396-019-0503-z. Epub 2019 Sep 6. link
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99. Albuminuria, the High-Density Lipoprotein Proteome, and Coronary Artery Calcification in Type 1 Diabetes Mellitus. Shao B, Zelnick LR, Wimberger J, Himmelfarb J, Brunzell J, Davidson WS, Snell-Bergeon JK, Bornfeldt KE, de Boer IH, Heinecke JW. Arterioscler Thromb Vasc Biol. 2019 Jul;39(7):1483-1491. doi: 10.1161/ATVBAHA.119.312556. Epub 2019 May 16. link
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101. Proteome-wide Analysis of Cellular Response to Ultraviolet Light for Biomaterial Synthesis and Modification. Ruskowitz ER, DeForest CA. ACS Biomater. Sci. Eng. 2019 Apr 5; 5, 2111-2116. link
102. Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ. Autophagy. 2019 Sep;15(9):1592-1605. doi: 10.1080/15548627.2019.1586258. Epub 2019 Mar 21. link
103. 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
104. Metabolism as an early predictor of DPSCs aging. Macrin D, Alghadeer A, Zhao YT, Miklas JW, Hussein AM, Detraux D, Robitaille AM, Madan A, Moon RT, Wang Y, Devi A, Mathieu J, Ruohola-Baker H. Sci Rep. 2019 Feb 18;9(1):2195. doi: 10.1038/s41598-018-37489-4. link
105. Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency. Mathieu J, Detraux D, Kuppers D, Wang Y, Cavanaugh C, Sidhu S, Levy S, Robitaille AM, Ferreccio A, Bottorff T, McAlister A, Somasundaram L, Artoni F, Battle S, Hawkins RD, Moon RT, Ware CB, Paddison PJ, Ruohola-Baker H. Nat Commun. 2019 Feb 7;10(1):632. doi: 10.1038/s41467-018-08020-0. link
106. 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 DN, Deutsch EW, Kappe SHI, Moritz RL. J Proteome Res. 2019 Feb 1;18(2):652-663. doi: 10.1021/acs.jproteome.8b00638. Epub 2018 Dec 21. link
107. 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. 2019 Feb 1;29(2):505-516. doi: 10.1093/cercor/bhx333. Erratum in: Cereb Cortex. 2019 Mar link
108. Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Venkataraman, Y.R., Timmins-Schiffman, E., Horwith, M.J., Lowe, A.T., Nunn, B., Vadopalas, B., Spencer, L.H., and Roberts, S.B. Mar Ecol Prog Ser 610, 65-81. 2019 Feb 1. link
109. Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates. Riffle M, Jaschob D, Zelter A, Davis TN. J Proteome Res. 2019 Feb 1;18(2):759-764. doi: 10.1021/acs.jproteome.8b00726. Epub 2018 Dec 19. link
110. Adaptations of Atribacteria to life in methane hydrates: hot traits for cold life. Glass, J., Blanchard, J., Ranjan, P., Kretz, C.B., Nunn, B.L., Johnson, A.M., McManus, J., and Stewart., F.J. bioRxiv. 2019 link

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111. Tools for 3D Interactome Visualization. Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE. J Proteome Res. 2019 Feb 1;18(2):753-758. doi: 10.1021/acs.jproteome.8b00703. Epub 2018 Dec 18. link
112. 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:e37688. doi: 10.7554/eLife.37688. link
113. 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
114. 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 Nov 15;175(5):1380-1392.e14. doi: 10.1016/j.cell.2018.09.037. Epub 2018 Oct 18. link
115. Variations in Copepod Proteome and Respiration Rate in Association with Diel Vertical Migration and Circadian Cycle. Maas AE, Blanco-Bercial L, Lo A, Tarrant AM, Timmins-Schiffman E. Biol Bull. 2018 Aug;235(1):30-42. doi: 10.1086/699219. Epub 2018 Aug 16. link
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118. 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
119. Mango: A general tool for CID-cleavable cross-linked peptide identification. Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Anal Chem. 2018 May 15;90(10):6028-6034. doi: 10.1021/acs.analchem.7b04991. Epub 2018 Apr 27. link
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125. 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
126. 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
127. 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
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129. 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
130. 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
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134. 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
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139. 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
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141. 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
142. 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
143. 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
144. 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
145. 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
146. 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
147. 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
148. 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
149. 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
150. 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

151. 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
152. CNS tau efflux via exosomes is likely increased in Parkinson disease but not in Alzheimer disease. Min Shi, Andrej Kovac, Ane Korff, Travis J. Cook, Carmen Ginghina, Kristin M. Bullock, Li Yang, Tessandra Stewart, Danfeng Zheng, Patrick Aro, Anzari Atik, Kathleen F. Kerr, Cyrus P. Zabetian, Elaine R. Peskind, Shu-Ching Hu, Joseph F. Quinn, Douglas R. Galasko, Thomas J. Montine, William A. Banks, Jing Zhang Alzheimers Dement. 2016 Nov; 12(11): 1125–1131. Published online 2016 May 24. link
153. 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
154. 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
155. 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
156. 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
157. 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
158. 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
159. In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Chavez JD, Schweppe DK, Eng JK, Bruce JE. Cell Chem Biol. 2016 Jun 23. link
160. 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
161. 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
162. 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
163. 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
164. 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
165. 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
166. 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

     2015

167. 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
168. 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
169. 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
170. 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
171. 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
172. 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
173. Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry. Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR. J Proteomics Bioinform 2015; 8(10): 231–239. doi: 10.4172/jpb.1000374. link
174. 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
175. 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
176. 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
177. 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
178. 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
179. 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
180. 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
181. 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
182. 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
183. 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
184. 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
185. 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
186. 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
187. 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
188. 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
189. 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
190. 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

     2014

191. 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
192. 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
193. 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
194. 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
195. 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
196. 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
197. 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
198. 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
199. 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
200. 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
201. 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
202. 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

     2013

203. 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
204. 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
205. 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
206. 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
207. 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
208. 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
209. 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
210. 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
211. 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
212. 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
213. 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
214. 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
215. 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

     2012

216. 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
217. 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
218. 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
219. 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
220. 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
221. 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
222. 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
223. 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
224. 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
225. 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
226. 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
227. 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
228. 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
229. 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
230. 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
231. 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
232. 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
233. 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
234. 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
235. 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
236. 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
237. 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

     2011

238. 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
239. 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
240. 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
241. 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
242. 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
243. 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
244. 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
245. 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
246. 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
247. 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
248. 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
249. 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
250. 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
251. 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
252. 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
253. PAcIFIC goes faster, quantitative and accurate. Alexandre Panchaud, Sunhee Jung, Scott A. Shaffer, John D. Aitchison, David R. Goodlett Anal Chem. 2011 Mar 15; 83(6): 2250–2257. Published online 2011 Feb 22. link
254. 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
255. 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
256. 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
257. 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
258. 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
259. 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

     2010

260. 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
261. 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
262. 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
263. 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
264. 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
265. 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
266. 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
267. 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
268. 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
269. 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
270. 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
271. 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
272. 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

     2009

273. Proteomics data repositories. Riffle M, Eng JK. Proteomics. 2009 Oct;9(20):4653-63. link
274. 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
275. 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
276. 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
277. 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

     2008

278. 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
279. 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
280. 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
281. 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