Stefani Thomas, PhD

Assistant Professor, Department of Laboratory Medicine and Pathology

Stefani Thomas

Contact Info

Office Phone 612-624-1054

Mailing Address:
Mayo Mail Code 609
420 Delaware Street SE
Minneapolis , MN 55455

Clinical Chemistry Fellowship, Department of Pathology, Johns Hopkins University School of Medicine, 2017-2019

PhD, Pharmaceutical Sciences, University of Southern California, 2007

BA, Biological Sciences, Music Minor, Dartmouth College, 2001

Postdoctoral Research Fellowship, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 2011


Dr. Thomas is a clinical chemist and a faculty member of the Advanced Research and Diagnostics Laboratory (ARDL) and a member of the Masonic Cancer Center.  She is also the Associate Medical Director of the West Bank Laboratory.  Motivated by the growing prevalence of mass spectrometry in the clinical laboratory, Thomas applies discovery and targeted proteomics methods to elucidate the biology of ovarian cancer and analyze proteins derived from alterations in cancer genomes and related biological processes. 

Thomas Research Lab


Mass spectrometry, clinical proteomics, analytical chemistry

Awards & Recognition

  • CTSI / Medical School Early Career Research Award, University of Minnesota, 2019
  • Young Investigator Award in Clinical Science (1st place), Johns Hopkins University School of Medicine, Department of Pathology, 2019
  • Young Investigator Travel Grant, Mass Spectrometry: Applications to the Clinical Laboratory 11th Annual Conference; Palm Springs, CA, 2019
  • Student Travel Grant, American Association for Clinical Chemistry 70th Annual Scientific Meeting, 2018
  • Young Investigator Award in Translational Science, Johns Hopkins University School of Medicine, Department of Pathology, 2018
  • Outstanding Poster Award, Shimadzu Global Innovation Summit; Kyoto, Japan, 2017
  • Young Investigator Award in Basic Science, Johns Hopkins University School of Medicine, Department of Pathology, 2013
  • Society for Neuroscience Minority Neuroscience Pre-doctoral Fellowship (NIH NRSA T32 award), 2004-2006
  • Outstanding Research Assistant Award, University of Southern California Department of Pharmaceutical Sciences, 2004

Professional Associations

  • American Society for Mass Spectrometry
  • Human Proteome Organization
  • American Association for Clinical Chemistry



WO 2013059786.  “Methylated peptides derived from tau protein and their antibodies for diagnosis and therapy of Alzheimer’s disease."


Selected list of publications

A more comprehensive list of publications can be found here.

  • Figueiredo JC, Hirsch FR, Kushi LH, Nembhard WN, Crawford JM, Mantis N, Finster L, Merin NM, Merchant A, Reckamp KL, Melmed GY, Braun J, McGovern D, Parekh S, Corley DA, Zohoori N, Amick BC, Du R, Gregersen PK, Diamond B, Taioli E, Sariol C, Espino A, Weiskopf D, Gifoni A, Brien J, Hanege W, Lipsitch M, Zidar DA, Scheck McAlearney A, Wajnberg A, LaBaer J, Yvonne Lewis E, Binder RA, Moormann AM, Forconi C, Forrester S, Batista J, Schieffelin J, Kim D, Biancon G, VanOudenhove J, Halene S, Fan R, Barouch DH, Alter G, Pinninti S, Boppana SB, Pati SK, Latting M, Karaba AH, Roback J, Sekaly R, Neish A, Brincks AM, Granger DA, Karger AB, Thyagarajan B, Thomas SN, Klein SL, Cox AL, Lucas T, Furr-Holden D, Key K, Jones N, Wrammerr J, Suthar M, Yu Wong S, Bowman NM, Simon V, Richardson LD, McBride R, Krammer F, Rana M, Kennedy J, Boehme K, Forrest C, Granger SW, Heaney CD, Knight Lapinski M, Wallet S, Baric RS, Schifanella L, Lopez M, Fernández S, Kenah E, Panchal AR, Britt WJ, Sanz I, Dhodapkar M, Ahmed R, Bartelt LA, Markmann AJ, Lin JT, Hagan RS, Wolfgang MC, Skarbinski J. Mission, organization, and future direction of the Serological Sciences Network for COVID-19 (SeroNet) epidemiologic cohort studies. Open Forum Infect Dis. 2022 Apr 27;9(6):ofac171. doi: 10.1093/ofid/ofac171.
  • Karger AB, Brien JD, Christen JM, Dhakal S, Kemp TJ, Klein SL, Pinto LA, Premkumar L, Roback JD, Binder RA, Boehme KW, Boppana S, Cordon-Cardo C, Crawford JM, Daiss JL, Dupuis AP 2nd, Espino AM, Firpo-Betancourt A, Forconi C, Forrest JC, Girardin RC, Granger DA, Granger SW, Haddad NS, Heaney CD, Hunt DT, Kennedy JL, King CL, Krammer F, Kruczynski K, LaBaer J, Lee FE, Lee WT, Liu SL, Lozanski G, Lucas T, Mendu DR, Moormann AM, Murugan V, Okoye NC, Pantoja P, Payne AF, Park J, Pinninti S, Pinto AK, Pisanic N, Qiu J, Sariol CA, Simon V, Song L, Steffen TL, Stone ET, Styer LM, Suthar MS, Thomas SN, Thyagarajan B, Wajnberg A, Yates JL, Sobhani K. The Serological Sciences Network (SeroNet) for COVID-19: Depth and breadth of serology assays and plans for assay harmonization. mSphere. 2022 Jun 15:e0019322. doi: 10.1128/msphere.00193-22. 
  • Chaudhry S, Thomas SN, Simmons GE Jr.Targeting lipid metabolism in the treatment of ovarian cancer.
    Oncotarget. 2022 May 25;13:768-783. doi: 10.18632/oncotarget.28241. eCollection 2022.
  • Thomas SN, Karger AB, Altawallbeh G, Nelson KM, Jacobs DR Jr, Gorlin J, Barcelo H, Thyagarajan B. Ultrasensitive detection of salivary SARS-CoV-2 IgG antibodies in individuals with natural and COVID-19 vaccine-induced immunity.  Sci Rep. 2022 May 25;12(1):8890. doi: 10.1038/s41598-022-12869-z 
  • Ryu J, Thomas SN.  Quantitative mass spectrometry-based proteomics for biomarker development in ovarian cancer.  Molecules. 2021 May 3;26(9):2674. doi: 10.3390/molecules26092674.
  • Murthy V, Altawallbeh G, Larson-Nath C, Karger AB, Thomas SN. Transient hyperphosphatasemia following pediatric liver transplantation in a patient with hepatic and skeletal abnormalities.  Clin Chim Acta. 2021 Apr 4:S0009-8981(21)00115-7. doi: 10.1016/j.cca.2021.03.030. 
  • Thomas SN, Altawallbeh G, Zaun CP, Pape KA, Peters JM, Titcombe PJ, Dileepan T, Rapp MJ, Bold TD, Schacker TW, Arbefeville S, Ferrieri P, Thyagarajan B, Jenkins MK, Karger AB. Initial determination of COVID-19 seroprevalence among outpatients and healthcare workers in Minnesota using a novel SARS-CoV-2 total antibody ELISA. Clin Biochem. 2021 Feb 1:S0009-9120(21)00027-8. doi: 10.1016/j.clinbiochem.2021.01.010.
  • Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore FJ, Hu Y, Zhao R, Schnaubelt M, Keshishian H, Monroe ME, Zhang Z, Udeshi ND, Mani D, Davies SR, Townsend RR, Chan DW, Smith RD, Zhang H, Liu T, and Carr SA. (2018) Reproducible workflow for multiplexed deep-scale analysis of the proteome and phosphoproteome of tumor tissues by liquid chromatography-mass spectrometry.Nature Protocols.13:1632-1661. PMID: 29988108.
  • Zhou Z-Y, Chen L, Zhang B, Tian Y, Liu T, Thomas S, Chen L, Boja E, Hiltke T, Kinsinger C, Rodriguez H, Davies S, Li S, Snider J, Erdmann-Gilmore P, Tabb D, Townsend R, Ellis M, Rodland K, Smith R, Carr S, Zhang Z, Chan D, and Zhang H. (2017) Quality assessments of long-term quantitative proteomic analysis of tumor tissues.Journal of Proteome Research.16:4523-4530. PMID: 29124938.
  • Thomas SN, Chen L, Liu Y, Höti N, and Zhang H. (2017) Targeted proteomic analyses of Histone H4 acetylation changes associated with homologous recombination deficient high-grade serous ovarian carcinomas.Journal of Proteome Research.16:3704-3710. PMID: 28866885.
  • Collins BC, Hunter C, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson B, Gingras A-C, Held JM, Hirayama M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy M, Moritz R, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng S-C, Zhang H, Aebersold R. (2017) Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH mass spectrometry.Nature Communications.8:291. PMID: 28827567.
  • Yang S, Zhang L, Thomas S, Hu Y, Li S, Cipollo J, and Zhang H. (2017) Modification of sialic acids on solid-phase: accurate characterization of protein sialylation.Analytical Chemistry.89:6330-6335. PMID: 28505427.
  • Chen Z, Dempsey DR, Thomas SN, Hayward D, Bolduc DM, and Cole PA. (2016) Molecular features of PTEN regulation by C-terminal phosphorylation.Journal of Biological Chemistry.291:14160-14169. PMID: 27226612.
  • Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou J-Y, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Choi C, Monroe ME, Thomas S, Moore RJ, Yu K-H, Tabb DL, Fenyo? D, Bafna V, Wang Y, Rodriquez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih I-M, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD. (2016) Integrated proteogenomic characterization of human high grade serious ovarian cancer.Cell.166:755-765. PMID: 27372738.
  • Hoofnagle A, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian W-J, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk J, Wong S, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, and Paulovich AG. (2016) Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays.Clinical Chemistry62:48-69. PMID: 26719571.
  • Thomas SN, Harlan R, Chen J, Aiyetan P, Liu Y, Sokoll L, Aebersold R, Chan DW, and Zhang H. (2015) Multiplexed targeted mass spectrometry based assays for the quantification of N-linked glycosite-containing peptides in serum.Analytical Chemistry.87:10830-10838.PMID: 26451657.
  • Thomas SN, Zhang H, and Cotter R. (2015). Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues.Clinical Proteomics12. PMID: 26019700.
  • Funk K, Thomas SN, Schafer KN, Cooper GL, Liao Z, Clark DJ, Yang AJ, and Kuret J. (2014) Lysine methylation is an endogenous post-translational modification of tau protein in human brain and a modulator of aggregation propensity.Biochemical Journal.462:77-88. PMID: 24869773.
  • Thomas SN, Liao Z, Clark D, Chen Y, Samadani R, Mao L, Ann DK, Baulch JE, Shapiro P, and Yang AJ. (2013) Exosomal proteome profiling: A potential multi-marker cellular phenotyping tool to characterize hypoxia-induced radiation resistance in breast cancer.Proteomes1: 87-108. PMID: 24860738.
  • Thomas SN, Morgan WF, Yang AJ, and Baulch JE. (2012) Quantitative proteomic analysis of mitochondrial proteins reveals pro-survival mechanisms in the perpetuation of radiation induced genomic instability.Free Radical Biology and Medicine53:618-628. PMID: 22569412.
  • Thomas SN, Funk KE, Wan Y, Liao Z, Davies P, Kuret J, and Yang AJ. (2012) Dual modification of Alzheimer’s disease PHF-tau protein by lysine methylation and ubiquitylation: a mass spectrometry approach.Acta Neuropathologica123:105-117. PMID: 22033876.
  • Thomas SN, Wan Y, Liao Z, Hanson PI, Yang AJ. (2011) Stable isotope labeling with amino acids in cell culture based mass spectrometry approach to detect transient protein interactions using substrate trapping.Analytical Chemistry83:5511-5518. PMID: 21619060.
  • Wan Y, Cripps D, Thomas S, Campbell P, Ambulos N, Chen T, and Yang A. (2008) PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information.Journal of Proteome Research7: 2803-2811. PMID: 18549264.
  • Cripps D,Thomas SN, Jeng Y, Davies P, and Yang AJ. (2006) Alzheimer's-disease-specific conformation of hyperphosphorylated phf-tau is polyubiquitinated through lys-48, lys-11, and lys-6 ubiquitin conjugation. Journal of Biological Chemistry281:10825-10838. PMID: 16443603.
  • Thomas SN, Soreghan BA, Nistor M, Sarsoza F, Head E, and Yang AJ. (2005) Reduced neuronal expression of synaptic transmission modulator HNK-1/Neural cell adhesion molecule (NCAM) as a potential consequence of Aß-mediated oxidative stress: a proteomic approach.Journal of Neurochemistry92: 705-717. PMID: 15686472.
  • Soreghan BA, Yang F, Thomas SN, Hsu J, and Yang AJ. (2003) High throughput proteomic-based identification of oxidatively induced protein carbonylation in mouse brain.Pharmaceutical Research20: 1713-1720. PMID: 14661913.   


Board Certifications

American Board of Clinical Chemistry

National Registry of Certified Chemists - Clinical Chemistry