Sophie Alvarez Y Albala


·Center for Biotechnology – Proteomics and Metabolomics

Sophie Alvarez

Research Professor

Area of Expertise: Plant Physiology, Weed, and Production Systems



Ph.D. PLANT BIOLOGY, University of LILLE 1 (FRANCE), 2004

Area of Focus

  • Mass Spectrometry-based Proteomics and Metabolomics

Research Interests

My research interest lies in developing and applying new proteomics and metabolomics methods using liquid-chromatography mass spectrometry to study a broad range of fields and applications, including crop breeding, plant biotechnology, food processing, biomarker discovery, toxicology and pharmacology. As the director of the Proteomics & Metabolomics facility at the Center for Biotechnology, University of Nebraska-Lincoln, I serve the scientific community in providing tools and expertise in the fields of proteomics and metabolomics, and establishing specialized methods for the analysis of proteins and a wide range of metabolites.


ResearchGate publication list
Book Chapters
  • Alvarez S and Naldrett MJ. Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics. In: Adv Exp Med Biol. Mirzaei, H and Carrasco, M (Editors). Springer 2016, 919, 63-81
  • Alvarez S. and Hicks L.M. Survey in Plant Root Proteomics: To Know the Unknown. In: Sustainable Agriculture and New Biotechnologies. Benkeblia N (Editor). CRC Press, Boca Raton (FL), 2011, 215-256.
Research Articles
  • Alvarez S, Naldrett MJ. Mass spectrometry based untargeted metabolomics for plant systems biology. Emerg Top Life Sci. 2021 Mar 11:ETLS20200271. doi: 10.1042/ETLS20200271.
  • Chen X, Liu B, Li X, An TT, Zhou Y, Li G, Wu-Smart J, Alvarez S, Naldrett MJ, Eudy J, Kubik G, Wilson RA, Kachman SD, Cui J, Yu J. Identification of anti- inflammatory vesicle-like nanoparticles in honey. J Extracell Vesicles. 2021 Feb;10(4):e12069. doi: 10.1002/jev2.12069.
  • Nolasco E, Yang J, Ciftci O, Vu DC, Alvarez S, Purdum S, Majumder K. Evaluating the effect of cooking and gastrointestinal digestion in modulating the bio-accessibility of different bioactive compounds of eggs. Food Chem. 2021 May 15;344:128623. doi: 10.1016/j.foodchem.2020.128623.
  • Rao PS, Nolasco E, Handa A, Naldrett MJ, Alvarez S, Majumder K. Effect of pH and Heat Treatment on the Antioxidant Activity of Egg White Protein-Derived Peptides after Simulated In-Vitro Gastrointestinal Digestion. Antioxidants (Basel). 2020 Nov 11;9(11):1114. doi: 10.3390/antiox9111114.
  • Zogli P, Alvarez S*, Naldrett MJ, Palmer NA, Koch KG, Pingault L, Bradshaw JD, Twigg P, Heng-Moss TM, Louis J, Sarath G. Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum). Sci Rep. 2020 Sep 9;10(1):14842. doi: 10.1038/s41598-020-71828-8. * co-first author
  • Guha S, Paul C, Alvarez S, Mine Y, Majumder K. Dietary γ-Glutamyl Valine Ameliorates TNF-α-Induced Vascular Inflammation via Endothelial Calcium- Sensing Receptors. J Agric Food Chem. 2020 Aug 26;68(34):9139-9149. doi: 10.1021/acs.jafc.0c04526.
  • Jia S, Yobi A, Naldrett MJ, Alvarez S, Angelovici R, Zhang C, Holding DR. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. J Exp Bot. 2020 Oct 7;71(19):5880-5895. doi: 10.1093/jxb/eraa325.
  • Edwards RL, Heueck I, Lee SG, Shah IT, Miller JJ, Jezewski AJ, Mikati MO, Wang X, Brothers RC, Heidel KM, Osbourn DM, Burnham CD, Alvarez S, Fritz SA, Dowd CS, Jez JM, Odom John AR. Potent, specific MEPicides for treatment of zoonotic staphylococci. PLoS Pathog. 2020 Jun 4;16(6):e1007806. doi: 10.1371/journal.ppat.1007806.
  • Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, Jez JM. Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid. J Biol Chem. 2019 Nov 8;294(45):16855-16864. doi: 10.1074/jbc.RA119.009949.
  • Lagundžin D, Hu WF, Law HCH, Krieger KL, Qiao F, Clement EJ, Drincic AT, Nedić O, Naldrett MJ, Alvarez S, Woods NT. Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactome. PLoS One. 2019 Aug 28;14(8):e0220568. doi: 10.1371/journal.pone.0220568.
  • Shihabudeen Haider Ali MS, Cheng X, Moran M, Haemmig S, Naldrett MJ, Alvarez S, Feinberg MW, Sun X. LncRNA Meg3 protects endothelial function by regulating the DNA damage response. Nucleic Acids Res. 2019 Feb 20;47(3):1505-1522. doi: 10.1093/nar/gky1190.
  • Wang X, Edwards RL, Ball H, Johnson C, Haymond A, Girma M, Manikkam M, Brothers RC, McKay KT, Arnett SD, Osbourn DM, Alvarez S, Boshoff HI, Meyers MJ, Couch RD, Odom John AR, Dowd CS. MEPicides: α,β-Unsaturated Fosmidomycin Analogues as DXR Inhibitors against Malaria. J Med Chem. 2018 Oct 11;61(19):8847-8858. doi: 10.1021/acs.jmedchem.8b01026.
  • Sherp AM, Westfall CS, Alvarez S, Jez JM. Arabidopsis thaliana GH3.15 acyl acid amido synthetase has a highly specific substrate preference for the auxin precursor indole-3-butyric acid. J Biol Chem. 2018 Mar 23;293(12):4277-4288. doi: 10.1074/jbc.RA118.002006.
  • Westfall CS, Sherp AM, Zubieta C, Alvarez S, Schraft E, Marcellin R, Ramirez L, Jez JM. Arabidopsis thaliana GH3.5 acyl acid amido synthetase mediates metabolic crosstalk in auxin and salicylic acid homeostasis. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13917-13922. doi: 10.1073/pnas.1612635113.
  • Para A, Muhammad D, Orozco-Nunnelly DA, Memishi R, Alvarez S, Naldrett MJ, Warpeha KM. The Dehydratase ADT3 Affects ROS Homeostasis and Cotyledon Development. Plant Physiol. 2016 Oct;172(2):1045-1060. doi: 10.1104/pp.16.00464.
  • Huang H, Alvarez S, Nusinow DA. Data on the identification of protein interactors with the Evening Complex and PCH1 in Arabidopsis using tandem affinity purification and mass spectrometry (TAP-MS). Data Brief. 2016 May 14;8:56-60. doi: 10.1016/j.dib.2016.05.014. PMID: 27274533; PMCID: PMC4885145.
  • Huang H, Alvarez S, Bindbeutel R, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics. 2016 Jan;15(1):201-17. doi: 10.1074/mcp.M115.054064. Epub 2015 Nov 6.
  • Alvarez S, Roy Choudhury S, Sivagnanam K, Hicks LM, Pandey S. Quantitative Proteomics Analysis of Camelina sativa Seeds Overexpressing the AGG3 Gene to Identify the Proteomic Basis of Increased Yield and Stress Tolerance. J Proteome Res. 2015 Jun 5;14(6):2606-16. doi: 10.1021/acs.jproteome.5b00150.
  • Slade WO, Werth EG, McConnell EW, Alvarez S, Hicks LM. Quantifying reversible oxidation of protein thiols in photosynthetic organisms. J Am Soc Mass Spectrom. 2015 Apr;26(4):631-40. doi: 10.1007/s13361-014-1073-y.
  • Alvarez S, Roy Choudhury S, Pandey S. Comparative quantitative proteomics analysis of the ABA response of roots of drought-sensitive and drought-tolerant wheat varieties identifies proteomic signatures of drought adaptability. J Proteome Res. 2014 Mar 7;13(3):1688-701. doi: 10.1021/pr401165b.
  • Alvarez S, Roy Choudhury S, Hicks LM, Pandey S. Quantitative proteomics- based analysis supports a significant role of GTG proteins in regulation of ABA response in Arabidopsis roots. J Proteome Res. 2013 Mar 1;12(3):1487-501. doi: 10.1021/pr301159u. Epub 2013 Feb 4. PMID: 23336595.
  • Martyniuk CJ, Alvarez S. Proteome analysis of the fathead minnow (Pimephales promelas) reproductive testes. J Proteomics. 2013 Feb 21;79:28-42. doi: 10.1016/j.jprot.2012.11.023. Epub 2012 Dec 9. PMID: 23234800.
  • Sun F, Ding Y, Ji Q, Liang Z, Deng X, Wong CC, Yi C, Zhang L, Xie S, Alvarez S, Hicks LM, Luo C, Jiang H, Lan L, He C. Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15461-6. doi: 10.1073/pnas.1205952109.
  • Sun F, Liang H, Kong X, Xie S, Cho H, Deng X, Ji Q, Zhang H, Alvarez S, Hicks LM, Bae T, Luo C, Jiang H, He C. Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9095-100. doi: 10.1073/pnas.1200603109.
  • Wang H, Alvarez S, Hicks LM. Comprehensive comparison of iTRAQ and label- free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering. J Proteome Res. 2012 Jan 1;11(1):487-501. doi: 10.1021/pr2008225.
  • Wang H, Wang S, Lu Y, Alvarez S, Hicks LM, Ge X, Xia Y. Proteomic analysis of early-responsive redox-sensitive proteins in Arabidopsis. J Proteome Res. 2012 Jan 1;11(1):412-24. doi: 10.1021/pr200918f.
  • Alvarez S, Hicks LM, Pandey S. ABA-dependent and -independent G-protein signaling in Arabidopsis roots revealed through an iTRAQ proteomics approach. J Proteome Res. 2011 Jul 1;10(7):3107-22. doi: 10.1021/pr2001786.
  • Alvarez S, Galant A, Jez JM, Hicks LM. Redox-regulatory mechanisms induced by oxidative stress in Brassica juncea roots monitored by 2-DE proteomics. Proteomics. 2011 Apr;11(7):1346-50. doi: 10.1002/pmic.201000450.
  • Ernst L, Goodger JQ, Alvarez S, Marsh EL, Berla B, Lockhart E, Jung J, Li P, Bohnert HJ, Schachtman DP. Sulphate as a xylem-borne chemical signal precedes the expression of ABA biosynthetic genes in maize roots. J Exp Bot. 2010 Jul;61(12):3395-405. doi: 10.1093/jxb/erq160.
  • Waller JC, Alvarez S, Naponelli V, Lara-Nuñez A, Blaby IK, Da Silva V, Ziemak MJ, Vickers TJ, Beverley SM, Edison AS, Rocca JR, Gregory JF 3rd, de Crécy-Lagard V, Hanson AD. A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10412-7. doi: 10.1073/pnas.0911586107.
  • Marsh E, Alvarez S, Hicks LM, Barbazuk WB, Qiu W, Kovacs L, Schachtman D. Changes in protein abundance during powdery mildew infection of leaf tissues of Cabernet Sauvignon grapevine (Vitis vinifera L.). Proteomics. 2010 May;10(10):2057-64. doi: 10.1002/pmic.200900712.
  • Alvarez S, Zhu M, Chen S. Proteomics of Arabidopsis redox proteins in response to methyl jasmonate. J Proteomics. 2009 Nov 2;73(1):30-40. doi: 10.1016/j.jprot.2009.07.005.
  • Kavazis AN, Alvarez S, Talbert E, Lee Y, Powers SK. Exercise training induces a cardioprotective phenotype and alterations in cardiac subsarcolemmal and intermyofibrillar mitochondrial proteins. Am J Physiol Heart Circ Physiol. 2009 Jul;297(1):H144-52. doi: 10.1152/ajpheart.01278.2008.
  • Alvarez S, Berla BM, Sheffield J, Cahoon RE, Jez JM, Hicks LM. Comprehensive analysis of the Brassica juncea root proteome in response to cadmium exposure by complementary proteomic approaches. Proteomics. 2009 May;9(9):2419-31. doi: 10.1002/pmic.200800478.
  • Alvarez S, Wilson GH, Chen S. Determination of in vivo disulfide-bonded proteins in Arabidopsis. J Chromatogr B Analyt Technol Biomed Life Sci. 2009 Jan 1;877(1-2):101-4. doi: 10.1016/j.jchromb.2008.11.027. Epub 2008 Nov 21. PMID: 19058769.
  • Alvarez S, He Y, Chen S. Comparative investigations of the glucosinolate- myrosinase system in Arabidopsis suspension cells and hypocotyls. Plant Cell Physiol. 2008 Mar;49(3):324-33. doi: 10.1093/pcp/pcn007.
  • Alvarez S, Marsh EL, Schroeder SG, Schachtman DP. Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant Cell Environ. 2008 Mar;31(3):325-40. doi: 10.1111/j.1365-3040.2007.01770.x.
  • Zhu J, Alvarez S, Marsh EL, Lenoble ME, Cho IJ, Sivaguru M, Chen S, Nguyen HT, Wu Y, Schachtman DP, Sharp RE. Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit. Plant Physiol. 2007 Dec;145(4):1533-48. doi: 10.1104/pp.107.107250.
  • Alvarez S, Goodger JQ, Marsh EL, Chen S, Asirvatham VS, Schachtman DP. Characterization of the maize xylem sap proteome. J Proteome Res. 2006 Apr;5(4):963-72. doi: 10.1021/pr050471q.
  • Zhu J, Chen S, Alvarez S, Asirvatham VS, Schachtman DP, Wu Y, Sharp RE. Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins. Plant Physiol. 2006 Jan;140(1):311-25. doi: 10.1104/pp.105.070219.