Publications

Publications from the TaMADOR consortium supported by:

• U01 DK137097 (University of Washington)
• U01 DK137113 (Pacific Northwest National Laboratories)
• U01 DK124020 (Pacific Northwest National Laboratories)
• U01 DK124019 (Cedars-Sinai Medical Center)

Publication Metrics

Last updated: February 04, 2026 — 52 publications

• Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes
  Kelly S, Sarkar S, Williams SM, Fu AD, Butterworth EA, Sagendorf TJ, Nierves LA, Kwon Y, Li X, Petyuk VA, Chen J, Nakayasu ES, Atkinson MA, Kulkarni RN, Mathews CE, Zhu Y, Campbell-Thompson M, Qian WJ
  bioRxiv : the preprint server for biology, 2025
  PubMed DOI
• Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists
  Hsu C, Shulman N, Stewart HI, Petzoldt J, Pashkova A, Plubell DL, Denisov E, Hagedorn B, Damoc NE, MacLean BX, Remes PM, Canterbury JD, Makarov AA, Hock C, Zabrouskov V, Wu CC, MacCoss MJ
  Journal of proteome research, 2025
  PubMed DOI
• Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort
  Fu Q, Remes PM, Lee J, Jacob C, Li D, Vegesna M, Raedschelders K, Haghani A, Mengesha E, Debbas P, Hoedt E, Joung S, Cheng S, Peterman S, Fert-Bober J, Melmed GY, McGovern DPB, Murray CI, Van Eyk JE
  Angewandte Chemie (International ed. in English), 2025
  PubMed DOI
• Characterization of Cytokine Treatment on Human Pancreatic Islets by Top-Down Proteomics
  Ives AN, Sagendorf TJ, Nierves L, Lin TT, Dirice E, Kulkarni RN, Paša-Tolić L, Qian WJ, Fulcher JM
  Proteomics, 2025
  PubMed DOI
• The current status of serum insulin measurements and the need for standardization
  Rohlfing C, Petroski G, Hatten-Beck M, Hanson S, Hoofnagle AN, Little RR, Kabytaev K
  Clinical chemistry and laboratory medicine, 2025
  PubMed DOI
• Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome
  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
  Nature communications, 2025
  PubMed DOI
• Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics - Beyond identification lists
  Hsu C, Shulman N, Stewart H, Petzoldt J, Pashkova A, Plubell DL, Denisov E, Hagedorn B, Damoc E, MacLean BX, Remes P, Canterbury JD, Makarov A, Hock C, Zabrouskov V, Wu CC, MacCoss MJ
  bioRxiv : the preprint server for biology, 2025
  PubMed DOI
• Characterization of cytokine treatment on human pancreatic islets by top-down proteomics
  Ives AN, Sagendorf T, Nierves L, Lin TT, Dirice E, Kulkarni RN, Paša-Tolić L, Qian WJ, Fulcher JM
  bioRxiv : the preprint server for biology, 2025
  PubMed DOI
• Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer
  Plubell DL, Huang E, Spencer SE, Poston KL, Montine TJ, MacCoss MJ
  Journal of proteome research, 2025
  PubMed DOI
• The Need for Better Validation: Evaluating Aptamer and Proximity Extension Assays for Large-Scale Clinical Proteomics Studies
  Hoofnagle AN, MacCoss MJ
  Clinical chemistry, 2025
  PubMed DOI
• Open-Source and FAIR Research Software for Proteomics
  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
  Journal of proteome research, 2025
  PubMed DOI
• A targeted LC MS/MS assay of a health surveillance panel and its application to chronic kidney disease
  Fu Q, Johnson C, Inker LA, Van Eyk JE
  bioRxiv : the preprint server for biology, 2025
  PubMed DOI
• A multiplex assay of leptin, resistin, and adiponectin by immunoaffinity enrichment and targeted mass spectrometry
  Pu J, Yang X, Lin TT, Fillmore TL, Gritsenko MA, Kelly SS, Swensen AC, Shi T, Master SR, DeLany JP, Goodpaster BH, Qian WJ, Qu J
  Journal of mass spectrometry and advances in the clinical lab, 2025
  PubMed DOI
• Biomarkers, Proteoforms, and Mass Spectrometry-Based Assays for Diabetes Clinical Research
  Nierves LA, Lin TT, Moradian A, Shen Q, Sechi S, MacCoss MJ, Qu J, van Eyk JE, Hoofnagle AN, Qian WJ
  The Journal of clinical endocrinology and metabolism, 2025
  PubMed DOI
• Molecular Phenotyping With Proteomics
  Schweppe DK, Beliveau BJ, Hoofnagle AN
  JAMA, 2025
  PubMed DOI
• Insights into insulin analog cross-reactivity: a comparative study of Siemens Atellica and LC-MS/MS
  Li J, Hatten-Beck M, Lee JKY, Hoofnagle AN
  Endocrine, 2025
  PubMed DOI
• Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics
  Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ
  Journal of proteome research, 2024
  PubMed DOI
• A Proteomics Pipeline for Generating Clinical Grade Biomarker Candidates from Data-Independent Acquisition Mass Spectrometry (DIA-MS) Discovery
  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
  Angewandte Chemie (International ed. in English), 2024
  PubMed DOI
• 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
  Journal of proteome research, 2024
  PubMed DOI
• An Inflection Point in High-Throughput Proteomics with Orbitrap Astral: Analysis of Biofluids, Cells, and Tissues
  Hendricks NG, Bhosale SD, Keoseyan AJ, Ortiz J, Stotland A, Seyedmohammad S, Nguyen CDL, Bui JT, Moradian A, Mockus SM, Van Eyk JE
  Journal of proteome research, 2024
  PubMed DOI
• Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements
  Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BM, Nakayasu ES, Qian WJ, Metz TO
  Trends in molecular medicine, 2024
  PubMed DOI
• A Trapping-Micro-LC-FAIMS/dCV-MS Strategy for Ultrasensitive and Robust Targeted Quantification of Protein Drugs and Biomarkers
  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
  Analytical chemistry, 2024
  PubMed DOI
• Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer
  Plubell DL, Remes PM, Wu CC, Jacob CC, Merrihew GE, Hsu C, Shulman N, MacLean BX, Heil L, Poston K, Montine T, MacCoss MJ
  bioRxiv : the preprint server for biology, 2024
  PubMed DOI
• Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics
  Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ
  bioRxiv : the preprint server for biology, 2024
  PubMed DOI
• Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer
  Plubell DL, Huang E, Spencer SE, Poston K, Montine TJ, MacCoss MJ
  bioRxiv : the preprint server for biology, 2024
  PubMed DOI
• The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics?
  Jiang Y, DeBord D, Vitrac H, Stewart J, Haghani A, Van Eyk JE, Fert-Bober J, Meyer JG
  Journal of proteome research, 2024
  PubMed DOI
• An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues
  Hendricks NG, Bhosale SD, Keoseyan AJ, Ortiz J, Stotland A, Seyedmohammad S, Nguyen CDL, Bui J, Moradian A, Mockus SM, Van Eyk JE
  bioRxiv : the preprint server for biology, 2024
  PubMed DOI
• Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome
  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
  bioRxiv : the preprint server for biology, 2024
  PubMed DOI
• Interlaboratory Comparison of Antibody-Free LC-MS/MS Measurements of C-peptide and Insulin
  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
  Clinical chemistry, 2024
  PubMed DOI
• Proteomics of the heart
  Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE
  Physiological reviews, 2024
  PubMed DOI
• De novo design of high-affinity binders of bioactive helical peptides
  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
  Nature, 2024
  PubMed DOI
• High Doses of Exogenous Glucagon Stimulate Insulin Secretion and Reduce Insulin Clearance in Healthy Humans
  Gray SM, Goonatilleke E, Emrick MA, Becker JO, Hoofnagle AN, Stefanovski D, He W, Zhang G, Tong J, Campbell J, D'Alessio DA
  Diabetes, 2024
  PubMed DOI
• Top-Down Proteomics of Mouse Islets With Beta Cell CPE Deletion Reveals Molecular Details in Prohormone Processing
  Fulcher JM, Swensen AC, Chen YC, Verchere CB, Petyuk VA, Qian WJ
  Endocrinology, 2023
  PubMed DOI
• Transcriptome and secretome profiling of sensory neurons reveals sex differences in pathways relevant to insulin sensing and insulin secretion
  Moon S, Alsarkhi L, Lin TT, Inoue R, Tahiri A, Colson C, Cai W, Shirakawa J, Qian WJ, Zhao JY, El Ouaamari A
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 2023
  PubMed DOI
• Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity
  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
  Cell reports. Medicine, 2023
  PubMed DOI
• Deletion of Carboxypeptidase E in β-Cells Disrupts Proinsulin Processing but Does Not Lead to Spontaneous Development of Diabetes in Mice
  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
  Diabetes, 2023
  PubMed DOI
• Species-Deconvolved Proteomics for In Situ Investigation of Tumor-Stroma Interactions after Treatment of Pancreatic Cancer Patient-Derived Xenografts with Combined Gemcitabine and Paclitaxel
  Wang X, Niu J, Qian S, Shen S, Straubinger RM, Qu J
  Journal of proteome research, 2023
  PubMed DOI
• Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways
  Dakup PP, Feng S, Shi T, Jacobs JM, Wiley HS, Qian WJ
  Molecules (Basel, Switzerland), 2023
  PubMed DOI
• Targeted Mass Spectrometry Assays for Specific Quantification of Urinary proPSA Isoforms
  Kitata RB, Hu LY, Lin TT, Nicora CD, Fillmore TL, Nie S, Hudson RD, Liu T, Leach RJ, Liu AY, Qian WJ, Shi T
  Journal of proteome research, 2023
  PubMed DOI
• Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins
  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
  Cell metabolism, 2023
  PubMed DOI
• Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS
  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
  Analytical chemistry, 2023
  PubMed DOI
• High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation
  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
  Nature protocols, 2023
  PubMed DOI
• Mass spectrometry-based targeted proteomics for analysis of protein mutations
  Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T
  Mass spectrometry reviews, 2023
  PubMed DOI
• In-depth mapping of protein localizations in whole tissue by micro-scaffold assisted spatial proteomics (MASP)
  Ma M, Huo S, Zhang M, Qian S, Zhu X, Pu J, Rasam S, Xue C, Shen S, An B, Wang J, Qu J
  Nature communications, 2022
  PubMed DOI
• Apolipoprotein C3 and circulating mediators of preadipocyte proliferation in states of lipodystrophy
  Brasil BB, Masaji S, Martins BT, Jiang H, Song N, Athena A S, Lucas B, François M, Wei-Jun Q, Rohit KN, Ronald KC
  Molecular metabolism, 2022
  PubMed DOI
• A Pilot Study of Urine Proteomics in COVID-19-Associated Acute Kidney Injury
  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
  Kidney international reports, 2021
  PubMed DOI
• Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation
  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
  Nature protocols, 2021
  PubMed DOI
• Parallel, High-Quality Proteomic and Targeted Metabolomic Quantification Using Laser Capture Microdissected Tissues
  Shen S, Li J, Huo S, Ma M, Zhu X, Rasam S, Duan X, Qu M, Titus MA, Qu J
  Analytical chemistry, 2021
  PubMed DOI
• 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
  Wang X, Jin L, Hu C, Shen S, Qian S, Ma M, Zhu X, Li F, Wang J, Tian Y, Qu J
  Analytical chemistry, 2021
  PubMed DOI
• PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks
  Sundararaman N, Go J, Robinson AE, Mato JM, Lu SC, Van Eyk JE, Venkatraman V
  Journal of the American Society for Mass Spectrometry, 2020
  PubMed DOI
• Precision Medicine: Role of Proteomics in Changing Clinical Management and Care
  Van Eyk JE, Snyder MP
  Journal of proteome research, 2019
  PubMed DOI
• Precision Medicine
  Van Eyk JE, Sobhani K
  Circulation, 2018
  PubMed DOI

This list is updated periodically. For the most current list, please also see PubMed and individual research group pages.