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TaMADOR Publications

 

Publications from U01 DK137097, U01 DK137113, U01 DK124020, and U01 DK124019

  1. Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ. Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv [Preprint]. 2024 Apr 2:2023.06.10.544439. doi: 10.1101/2023.06.10.544439. PMID: 38617345; PMCID: PMC11014469.
  2. Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev. 2024 Jul 1;104(3):931-982. doi:10.1152/physrev.00026.2023. Epub 2024 Feb 1. PMID: 38300522.
  3. Fulcher JM, Swensen AC, Chen YC, Verchere CB, Petyuk VA, Qian WJ. Top-Down Proteomics of Mouse Islets With Beta Cell CPE Deletion Reveals Molecular Details in Prohormone Processing. Endocrinology. 2023 Nov 2;164(12):bqad160. doi: 10.1210/endocr/bqad160. PMID: 37967211; PMCID: PMC10650973.
  4. Rasam S, Lin Q, Shen S, Straubinger RM, Qu J. Highly Reproducible Quantitative Proteomics Analysis of Pancreatic Cancer Cells Reveals Proteome- Level Effects of a Novel Combination Drug Therapy That Induces Cancer Cell Death via Metabolic Remodeling and Activation of the Extrinsic Apoptosis Pathway. J Proteome Res. 2023 Dec 1;22(12):3780-3792. doi: 10.1021/acs.jproteome.3c00463. Epub 2023 Oct 31. PMID: 37906173.
  5. Moon S, Alsarkhi L, Lin TT, Inoue R, Tahiri A, Colson C, Cai W, Shirakawa J, Qian WJ, Zhao JY, El Ouaamari A. Transcriptome and secretome profiling of sensory neurons reveals sex differences in pathways relevant to insulin sensing and insulin secretion. FASEB J. 2023 Oct;37(10):e23185. doi:10.1096/fj.202300941R. PMID: 37695721; PMCID: PMC10503313.
  6. Nakayasu ES, Bramer LM, Ansong C, Schepmoes AA, Fillmore TL, Gritsenko MA, Clauss TR, Gao Y, Piehowski PD, Stanfill BA, Engel DW, Orton DJ, Moore RJ, Qian WJ, Sechi S, Frohnert BI, Toppari J, Ziegler AG, Lernmark Å, Hagopian W, Akolkar B, Smith RD, Rewers MJ, Webb-Robertson BM, Metz TO; TEDDY Study Group. Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity. Cell Rep Med. 2023 Jul 18;4(7):101093. doi: 10.1016/j.xcrm.2023.101093. Epub 2023 Jun 29. PMID:37390828; PMCID: PMC10394168.
  7. Chen YC, Taylor AJ, Fulcher JM, Swensen AC, Dai XQ, Komba M, Wrightson KLC, Fok K, Patterson AE, Klein Geltink RI, MacDonald PE, Qian WJ, Verchere CB. Deletion of Carboxypeptidase E in β-Cells Disrupts Proinsulin Processing but Does Not Lead to Spontaneous Development of Diabetes in Mice. Diabetes. 2023 Sep 1;72(9):1277-1288. doi: 10.2337/db22-0945. PMID: 37364047; PMCID: PMC10450824.
  8. Wang X, Niu J, Qian S, Shen S, Straubinger RM, Qu J. Species-Deconvolved Proteomics for In Situ Investigation of Tumor-Stroma Interactions after Treatment of Pancreatic Cancer Patient-Derived Xenografts with Combined Gemcitabine and Paclitaxel. J Proteome Res. 2023 Jul 7;22(7):2436-2449. doi: 10.1021/acs.jproteome.3c00164. Epub 2023 Jun 13. PMID: 37311110; PMCID: PMC10561664.
  9. Dakup PP, Feng S, Shi T, Jacobs JM, Wiley HS, Qian WJ. Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules. 2023 Jan 23;28(3):1143. doi: 10.3390/molecules28031143. PMID: 36770810; PMCID: PMC9919559.
  10. Kitata RB, Hu LY, Lin TT, Nicora CD, Fillmore TL, Nie S, Hudson RD, Liu T, Leach RJ, Liu AY, Qian WJ, Shi T. Targeted Mass Spectrometry Assays for Specific Quantification of Urinary proPSA Isoforms. J Proteome Res. 2023 Mar 3;22(3):942-950. doi: 10.1021/acs.jproteome.2c00745. Epub 2023 Jan 10. PMID: 36626706; PMCID: PMC10072162.
  11. Martinez TF, Lyons-Abbott S, Bookout AL, De Souza EV, Donaldson C, Vaughan JM, Lau C, Abramov A, Baquero AF, Baquero K, Friedrich D, Huard J, Davis R, Kim B, Koch T, Mercer AJ, Misquith A, Murray SA, Perry S, Pino LK, Sanford C, Simon A, Zhang Y, Zipp G, Bizarro CV, Shokhirev MN, Whittle AJ, Searle BC, MacCoss MJ, Saghatelian A, Barnes CA. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab. 2023 Jan 3;35(1):166-183.e11. doi: 10.1016/j.cmet.2022.12.004. PMID: 36599300; PMCID:PMC9889109.
  12. Pu J, Xue C, Huo S, Shen Q, Qu Y, Yang X, An B, Angel TE, Chen Z, Mehl JT, Tang H, Yang E, Sikorski TW, Qu J. Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS. Anal Chem. 2023 Jan 17;95(2):924-934. doi: 10.1021/acs.analchem.2c03473. Epub 2022 Dec 19. PMID: 36534410; PMCID: PMC10581745.
  13. Shen S, Wang X, Zhu X, Rasam S, Ma M, Huo S, Qian S, Zhang M, Qu M, Hu C, Jin L, Tian Y, Sethi S, Poulsen D, Wang J, Tu C, Qu J. High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation. Nat Protoc. 2023 Mar;18(3):700-731. doi: 10.1038/s41596-022-00780-w. Epub 2022 Dec 9. PMID: 36494494; PMCID: PMC10673696.
  14. Brasil BB, Masaji S, Martins BT, Jiang H, Song N, Athena A S, Lucas B, François M, Wei-Jun Q, Rohit KN, Ronald KC. Apolipoprotein C3 and circulating mediators of preadipocyte proliferation in states of lipodystrophy. Mol Metab. 2022 Oct;64:101572. doi: 10.1016/j.molmet.2022.101572. Epub 2022 Aug 11. PMID: 35964946; PMCID: PMC9418991.
  15. Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. Mass Spectrom Rev. 2023 Mar;42(2):796-821. doi: 10.1002/mas.21741. Epub 2021 Oct 31. PMID: 34719806; PMCID: PMC9054944.
  16. Ye Y, Swensen AC, Wang Y, Kaushal M, Salamon D, Knoten A, Nicora CD, Marks L, Gaut JP, Vijayan A, Orton DJ, Mudd PA, Parikh CR, Qian WJ, O'Halloran JA, Piehowski PD, Jain S. A Pilot Study of Urine Proteomics in COVID-19-Associated Acute Kidney Injury. Kidney Int Rep. 2021 Dec;6(12):3064-3069. doi: 10.1016/j.ekir.2021.09.010. Epub 2021 Oct 7. PMID: 34642644; PMCID: PMC8494995.
  17. Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BM, Metz TO. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc. 2021 Aug;16(8):3737-3760. doi:10.1038/s41596-021-00566-6. Epub 2021 Jul 9. PMID: 34244696; PMCID: PMC8830262.
  18. Shen S, Li J, Huo S, Ma M, Zhu X, Rasam S, Duan X, Qu M, Titus MA, Qu J. Parallel, High-Quality Proteomic and Targeted Metabolomic Quantification Using Laser Capture Microdissected Tissues. Anal Chem. 2021 Jun 29;93(25):8711-8718. doi: 10.1021/acs.analchem.1c01026. Epub 2021 Jun 10. PMID: 34110778; PMCID: PMC10640922.
  19. Wang X, Jin L, Hu C, Shen S, Qian S, Ma M, Zhu X, Li F, Wang J, Tian Y, Qu J. Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification. Anal Chem. 2021 Mar 23;93(11):4884-4893. doi: 10.1021/acs.analchem.0c05002. Epub 2021 Mar 9. PMID: 33687211; PMCID: PMC10666926.
  20. Sundararaman N, Go J, Robinson AE, Mato JM, Lu SC, Van Eyk JE, Venkatraman V. PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks. J Am Soc Mass Spectrom. 2020 Jul 1;31(7):1410-1421. doi: 10.1021/jasms.0c00032. Epub 2020 Jun 11. PMID: 32463229; PMCID: PMC10362945.
  21. Van Eyk JE, Sobhani K. Precision Medicine. Circulation. 2018 Nov 13;138(20):2172-2174. doi: 10.1161/CIRCULATIONAHA.118.036781. PMID: 30571512; PMCID: PMC8260056.
  22. Van Eyk JE, Snyder MP. Precision Medicine: Role of Proteomics in Changing Clinical Management and Care. J Proteome Res. 2019 Jan 4;18(1):1-6. doi: 10.1021/acs.jproteome.8b00504. Epub 2018 Oct 22. PMID: 30296097; PMCID: PMC10372929.