• Sign In

TaMADOR Publications

 

Publications from U01 DK137097, U01 DK137113, U01 DK124020, U01 DK121289 and U01 DK124019

 
  1. DK137097 | Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE. Open-Source and FAIR Research Software for Proteomics. J Proteome Res. 2025 May 2;24(5):2222-2234. doi: 10.1021/acs.jproteome.4c01079. Epub 2025 Apr 23. PMID: 40267229; PMCID: PMC12053954.
  2. DK124019 | Fu Q, Johnson C, Inker LA, Van Eyk JE. A targeted LC MS/MS assay of a health surveillance panel and its application to chronic kidney disease. bioRxiv [Preprint]. 2025 Mar 16:2025.03.14.643399. doi: 10.1101/2025.03.14.643399. PMID: 40161722; PMCID: PMC11952516.
  3. DK137097 | Schweppe DK, Beliveau BJ, Hoofnagle AN. Molecular Phenotyping With Proteomics. JAMA. 2025 Mar 11;333(10):898-899. doi: 10.1001/jama.2024.28089. PMID: 39883454; PMCID: PMC12053805.
  4. DK137097 | Li J, Hatten-Beck M, Lee JKY, Hoofnagle AN. Insights into insulin analog cross-reactivity: a comparative study of Siemens Atellica and LC-MS/MS. Endocrine. 2025 Jan;87(1):79-84. doi: 10.1007/s12020-024-03970-6. Epub 2024 Jul 19. PMID: 39030378; PMCID: PMC11739172.
  5. DK124019 | Fu Q, Vegesna M, Sundararaman N, Damoc E, Arrey TN, Pashkova A, Mengesha E, Debbas P, Joung S, Li D, Cheng S, Braun J, McGovern DPB, Murray CI, Xuan Y, Van Eyk JE. A Proteomics Pipeline for Generating Clinical Grade Biomarker Candidates from Data-Independent Acquisition Mass Spectrometry (DIA-MS) Discovery. Angew Chem Int Ed Engl. 2024 Dec 20;63(52):e202409446. doi: 10.1002/anie.202409446. Epub 2024 Nov 11. PMID: 39432331.
  6. DK137097 | Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ. Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics. J Proteome Res. 2024 Dec 6;23(12):5476-5486. doi: 10.1021/acs.jproteome.4c00599. Epub 2024 Oct 30. PMID: 39475161; PMCID: PMC11956834.
  7. DK137113 | Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BM, Nakayasu ES, Qian WJ, Metz TO. Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. Trends Mol Med. 2024 Dec;30(12):1137-1151. doi: 10.1016/j.molmed.2024.07.009. Epub 2024 Aug 15. PMID: 39152082; PMCID: PMC11631641.
  8. DK124019 | Hendricks NG, Bhosale SD, Keoseyan AJ, Ortiz J, Stotland A, Seyedmohammad S, Nguyen CDL, Bui J, Moradian A, Mockus SM, Van Eyk JE. An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues. bioRxiv [Preprint]. 2024 Apr 27:2024.04.26.591396. doi: 10.1101/2024.04.26.591396. Update in: J Proteome Res. 2024 Sep 6;23(9):4163-4169. doi: 10.1021/acs.jproteome.4c00384. PMID: 38712179; PMCID: PMC11071456.
  9. DK137113 DK124020 | Shen Q, Pu J, Xue C, Zhang M, Qu Y, Huo S, Belford M, Maxey C, Wijeratne N, Martins C, Peterman S, Qian WJ, Boeser C, Qu J. A Trapping-Micro-LC-FAIMS/dCV-MS Strategy for Ultrasensitive and Robust Targeted Quantification of Protein Drugs and Biomarkers. Anal Chem. 2024 Aug 13;96(32):13140-13149. doi: 10.1021/acs.analchem.4c01888. Epub 2024 Jul 30. PMID: 39078725; PMCID: PMC11984221.
  10. DK124019 | 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; PMCID: PMC11381016.
  11. DK137097 | Plubell DL, Remes PM, Wu CC, Jacob CC, Merrihew GE, Hsu C, Shulman N, MacLean BX, Heil L, Poston K, Montine T, MacCoss MJ. Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer. bioRxiv [Preprint]. 2024 Jun 11:2024.06.04.597431. doi: 10.1101/2024.06.04.597431. PMID: 38895256; PMCID: PMC11185584.
  12. DK124019 | Jiang Y, DeBord D, Vitrac H, Stewart J, Haghani A, Van Eyk JE, Fert-Bober J, Meyer JG. The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics? J Proteome Res. 2024 Jun 7;23(6):1871-1882. doi: 10.1021/acs.jproteome.4c00248. Epub 2024 May 7. PMID: 38713528; PMCID: PMC11161313.
  13. DK121289 DK137097 | Moradian A, Goonatilleke E, Lin TT, Hatten-Beck M, Emrick M, Schepmoes AA, Fillmore TL, MacCoss MJ, Sechi S, Sobhani K, Little R, Kabytaev K, van Eyk JE, Qian WJ, Hoofnagle AN. Interlaboratory Comparison of Antibody-Free LC-MS/MS Measurements of C-peptide and Insulin. Clin Chem. 2024 Jun 3;70(6):855-864. doi: 10.1093/clinchem/hvae034. PMID: 38549041; PMCID: PMC12052497.
  14. DK137097 | Plubell DL, Huang E, Spencer SE, Poston K, Montine TJ, MacCoss MJ. Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer. bioRxiv [Preprint]. 2024 May 30:2024.05.29.596554. doi: 10.1101/2024.05.29.596554. PMID: 38853953; PMCID: PMC11160738.
  15. DK121289 DK137097 | 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.
  16. DK121289 DK137097 | Gray SM, Goonatilleke E, Emrick MA, Becker JO, Hoofnagle AN, Stefanovski D, He W, Zhang G, Tong J, Campbell J, D'Alessio DA. High Doses of Exogenous Glucagon Stimulate Insulin Secretion and Reduce Insulin Clearance in Healthy Humans. Diabetes. 2024 Mar 1;73(3):412-425. doi: 10.2337/db23-0201. PMID: 38015721; PMCID: PMC10882148.
  17. DK121289 DK137097 | Vázquez Torres S, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D. De novo design of high-affinity binders of bioactive helical peptides. Nature. 2024 Feb;626(7998):435-442. doi: 10.1038/s41586-023-06953-1. Epub 2023 Dec 18. PMID: 38109936; PMCID: PMC10849960.
  18. DK124020 DK137113 | 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.
  19. DK124020 | 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.
  20. DK124020 | 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.
  21. DK124020 | 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.
  22. DK124020 | 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.
  23. DK124020 | 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.
  24. DK124020 | 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.
  25. DK124020 | 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.
  26. DK124020 | 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.
  27. DK124020 | 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.
  28. DK121289 | 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. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. 2023 Jan 6;51(D1):D1539-D1548. doi: 10.1093/nar/gkac1040. PMID: 36370099; PMCID: PMC9825490.
  29. DK137097 | 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.
  30. DK124020 | Ma M, Huo S, Zhang M, Qian S, Zhu X, Pu J, Rasam S, Xue C, Shen S, An B, Wang J, Qu J. In-depth mapping of protein localizations in whole tissue by micro-scaffold assisted spatial proteomics (MASP). Nat Commun. 2022 Dec 14;13(1):7736. doi: 10.1038/s41467-022-35367-2. PMID: 36517484; PMCID: PMC9751300.
  31. DK124020 | 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.
  32. DK121289 | Foulon N, Goonatilleke E, MacCoss MJ, Emrick MA, Hoofnagle AN. Multiplexed quantification of insulin and C-peptide by LC-MS/MS without the use of antibodies. J Mass Spectrom Adv Clin Lab. 2022 Jun 10;25:19-26. doi: 10.1016/j.jmsacl.2022.06.003. PMID: 35734440; PMCID: PMC9207678.
  33. DK121289 | Heil LR, Fondrie WE, McGann CD, Federation AJ, Noble WS, MacCoss MJ, Keich U. Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data. J Proteome Res. 2022 Jun 3;21(6):1382-1391. doi: 10.1021/acs.jproteome.1c00895. Epub 2022 May 12. PMID: 35549345; PMCID: PMC9204981.
  34. DK121289 | Phipps WS, Greene DN, Pflaum H, Laha TJ, Dickerson JA, Irvine J, Merrill AE, Ranjitkar P, Henderson CM, Hoofnagle AN. Small volume retinol binding protein measurement by liquid chromatography-tandem mass spectrometry. Clin Biochem. 2022 Jan;99:111-117. doi: 10.1016/j.clinbiochem.2021.10.005. Epub 2021 Oct 19. PMID: 34678307; PMCID: PMC8671195.
  35. DK124020 | 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.
  36. DK121289 | Martin K, Zhang T, Lin TT, Habowski AN, Zhao R, Tsai CF, Chrisler WB, Sontag RL, Orton DJ, Lu YJ, Rodland KD, Yang B, Liu T, Smith RD, Qian WJ, Waterman ML, Wiley HS, Shi T. Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. J Proteome Res. 2021 Sep 3;20(9):4452-4461. doi: 10.1021/acs.jproteome.1c00403. Epub 2021 Aug 5. PMID: 34351778; PMCID: PMC8945255.
  37. DK124020 | 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.
  38. DK124020 | 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.
  39. DK124020 | 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.
  40. DK121289 | Marcovina SM, Clouet-Foraison N, Koschinsky ML, Lowenthal MS, Orquillas A, Boffa MB, Hoofnagle AN, Vaisar T. Development of an LC-MS/MS Proposed Candidate Reference Method for the Standardization of Analytical Methods to Measure Lipoprotein(a). Clin Chem. 2021 Mar 1;67(3):490-499. doi: 10.1093/clinchem/hvaa324. PMID: 33517366; PMCID: PMC7935757.
  41. DK121289 | Owusu BY, Pflaum H, Garner R, Foulon N, Laha TJ, Hoofnagle AN. Development and Validation of a Novel LC-MS/MS Assay for C-Peptide in Human Serum. J Mass Spectrom Adv Clin Lab. 2021 Jan;19:1-6. doi: 10.1016/j.jmsacl.2020.12.001. Epub 2020 Dec 28. PMID: 34723236; PMCID: PMC8553002.
  42. DK124019 | 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.
  43. DK121289 | Pino LK, Searle BC, Yang HY, Hoofnagle AN, Noble WS, MacCoss MJ. Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics. J Proteome Res. 2020 Mar 6;19(3):1147-1153. doi: 10.1021/acs.jproteome.9b00666. Epub 2020 Feb 24. PMID: 32037841; PMCID: PMC7175947.
  44. DK124019 | 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.
  45. DK124019 | 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.