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Analytical Methods Research Group (AMR)

The mission of the Analytical Methods Research Group (AMR) is to improve the breadth and quality of composition data by developing, validating, and disseminating new analytical technologies that can be used in identifying and quantifying food components as well as verifying the identity of food materials.

  • Current Projects
  • Publications
  • Scientist Bios
  • Craig Byrdwell is an expert in analytical chemistry of lipids. His current projects include:
    • Applying new methods for analysis of complex food lipids, especially milk lipids, infant formula, and nutritional drinks, as well as lipids from agricultural products such as beans and others,
    • Applying lipidomic and metabolomics software tools for qualitative and quantitative analysis of complex lipid matrices in foods and agricultural products,
    • Quantitative analysis of Vitamin D and other fat-soluble vitamins in foods and agricultural products,
    • Developing liquid chromatography methods for lipid analysis using multiple mass spectrometers with different ionization techniques simultaneously in parallel,
    • Developing new two-dimensional chromatography techniques with multiple parallel mass spectrometry,
    • Developing groundbreaking three-dimensional chromatography techniques with parallel second dimensions for complex lipid analysis.
  • Pei Chen is an expert in the field of analytical chemistry and food and botanical chemistry. His current research projects include:
    • Development of a metabolomics platform for analysis of foods and botanicals,
    • Development of methodologies for validation of food and botanical identification methods based on chemometric methods,
    • Development of methodologies for non-targeted methods for food fraud adulteration,
    • Development of computer assisted “expert systems” for identification of secondary metabolites and generation of high-quality data for food components/nutrients databases.
  • James Harnly is an expert in the field of analytical chemistry and food and botanical chemistry. His current research projects include:
    • Administration of FoodData Central (FDC), the new USDA integrated, research focused data system,
    • Development of sampling methods for the Foundation Foods Data type,
    • Development of guidelines for validation of food and botanical identification methods based on chemometric methods,
    • Development of an integrated sample material and component analytical protocol based on fingerprinting, metabolomics, and DNA barcoding,
    • Development of non-targeted methods for food fraud adulteration.
  • Dave Luthria is an expert in the field of sample preparation and chromatography. His current research projects include:
    • Develop simplified spectroscopic fingerprints and multivariate analysis for the classification of foods based on cultivars, growing conditions, and nutrient quality traits.
    • Develop methods for separation and analysis of simple sugars and oligosaccharides from different food matrices by ion chromatographic coupled with pulse amperometry detection and liquid chromatographic methods coupled with mass spectrometry detector.
    • Develop methods for isolation and characterization of phytochemicals from different cultivars of foods (dry beans, soybeans, tomatoes, vegetables greens, grains, sweet potatoes) in different cultivars grown under different environmental conditions such as urban framing, different salinity, and growing locations.
    • Develop and validate analytical methods for the qualitative and quantitative analysis of targeted phytochemicals and dietary supplements.
      Craig Byrdwell Selected Publications:
  1. Byrdwell, W. C., "Comprehensive Dual Liquid Chromatography with Quadruple Mass Spectrometry (LC1MS2×LC1MS2 = LC2MS4) for Analysis of Parinari Curatellifolia and Other Seed Oil Triacylglycerols", Analytical Chemistry, 89(19):10537-10546 (2017), DOI: 10.1021/acs.analchem.7b02753.
  2. Byrdwell, W. C., "The Simulacrum System as a Construct for Mass Spectrometry of Triacylglycerols and Others", Lipids, 51(2):211-227 (2016), DOI: 10.1007/s11745-015-4101-1.
  3. Byrdwell, W. C., "The Updated Bottom Up Solution Applied to Mass Spectrometry of Soybean Oil in a Dietary Supplement Gelcap", Analytical and Bioanalytical Chemistry, 407(17):5143-5160 (2015), DOI: 10.1007/s00216-015-8590-9.
  4. Byrdwell, W. C., "Extract-Filter-Shoot Liquid Chromatography with Mass Spectrometry for the Analysis of Vitamin D2 in a Powdered Supplement Capsule and Standard Reference Material 3280", Journal of Separation Science, 37(16):2095-2110 (2014), DOI: 10.1002/jssc.201400234.
  5. Byrdwell, W.C., "Quadruple Parallel Mass Spectrometry Analysis of Vitamin D and Triacylglycerols in a Dietary Supplement", Journal of Chromatography A, 1320:48-65 (2013), DOI: 10.1016/j.chroma.2013.10.031.
  6. Byrdwell, W. C., Horst, R. L., Phillips, K. M., Holden, J. M., Patterson, K. Y., Harnly, J. M., Exler, J. "Vitamin D Levels in Fish and Shellfish Determined by Liquid Chromatography with Ultraviolet Detection and Mass Spectrometry", Journal of Food Composition and Analysis, 30(2):109-119 (2013), DOI: 10.1016/j.jfca.2013.01.005.
  7. Byrdwell, W. C., "Dilute-and-Shoot' Triple Parallel Mass Spectrometry Method for Analysis of Vitamin D and Triacylglycerols in Dietary Supplements", Analytical and Bioanalytical Chemistry, 401(10):3317-3334 (2011), DOI: 10.1007/s00216-011-5406-4.
  8. Byrdwell, W. C., "Dual Parallel Mass Spectrometry for Lipid and Vitamin D Analysis", Journal of Chromatography A, 1217(25):3992-4003 (2010), DOI: 10.1016/j.chroma.2009.11.101.
  9. Byrdwell, W. C., "Comparison of Analysis of Vitamin D3 in Foods Using Ultraviolet and Mass Spectrometric Detection", Journal of Agricultural and Food Chemistry, 57(6):2135-2146 (2009), DOI: 10.1021/jf803398u.
  10. Byrdwell, W.C., "Atmospheric Pressure Chemical Ionization Mass Spectrometry for Analysis of Lipids", Lipids, 36(4):327-346 (2001), DOI: 10.1007/s11745-001-0725-5.
      Pei Chen Selected Publications:
  1. Wu, X., Zhao, Y., Haytowitz, DB., Chen, P., and Pehrsson, PR. Effects of Domestic Cooking on Flavonoids in Broccoli and Calculation of Retention Factors. Heliyon. 5(3): e01310. 2019, DOI: 10.1016/j.heliyon.2019
  2. Sun, J, Zhang, M, Kubzdela, N, Luo, Y., Harnly, JM, and Chen, P. Determination of Variance of Secondary Metabolites in Lettuces Grown Under Different Light Sources by Flow Injection Mass Spectrometric (FIMS) Fingerprinting and ANOVA–PCA. J. Anal. Test. 2(4):312-321. 2018, DOI: 10.1007/s41664-018-0072-6
  3. Wang, Y, Vorsa, N, Harrington, PB, and Chen, P. Nontargeted Metabolomic Study on Variation of Phenolics in Different Cranberry Cultivars Using UPLC-IM – HRMS. J. Agri. Food Chem. 66:12206 – 12216. 2018, DOI: 10.1021/acs.jafc.8b05029.
  4. Harnly, J., Lu, Y., Sun, J. and Chen, P. Botanical supplements: Detecting the transition from ingredient to product. J. Food Comp. Anal. 64(1):85-92. 2017,
  5. Zhang, M., Sun, J., and Chen, P. Development of a Comprehensive Flavonoid Analysis Computational Tool for Ultrahigh-Performance Liquid Chromatography-Diode Array Detection-High-Resolution Accurate Mass-Mass Spectrometry Data. Anal. Chem. 89 (14), pp 7388–7397. 2017, DOI: 10.1021/acs.analchem.7b00771.
  6. Sun, J., Zhang, M., and Chen, P. GLS-Finder: An Automated Data-Mining System for Fast Profiling Glucosinolates and its Application in Brassica Vegetables. J. Agri. Food. Chem. 64 (21): 4407–4415. 2016, DOI: 10.1021/acs.jafc.6b01277.
  7. Zhang, M., Sun, J., and Chen, P. FlavonQ: An Automated Data Processing Tool for Profiling Flavone and Flavonol Glycosides with Ultra-High-Performance Liquid Chromatography−Diode Array Detection−High Resolution Accurate Mass−Mass Spectrometry. Anal. Chem. 87 (19):9974–9981. 2015, DOI: 10.1021/acs.analchem.5b02624.
  8. Sun, J. and Chen, P. Differentiation of Panax quinquefolius grown in the USA and China using LC/MS-based chromatographic fingerprinting and chemometric approaches. Anal. Bioanal. Chem. 399 (5):1877-1889. 2011, DOI: 10.1007/s00216-010-4586-7.
  9. Chen, P., Harnly, J. M., and Lester, G. E. Flow-injection mass spectral fingerprints demonstrate chemical differences in Rio Red grapefruit with respect to year, harvest time, and conventional versus organic farming. J. Agric. Food Chem. 58 (8):4545-4553. 2010, DOI:10.1021/jf904324c.
  10. Chen, P., Atkinson, R., and Wolf, W. R. Single-laboratory validation of a high-performance liquid chromatographic-diode array detector-fluorescence detector/mass spectrometric method for simultaneous determination of water-soluble vitamins in multivitamin dietary tablets. J. AOAC Int. 92 (2):680-687. 2009,
      James Harnly Selected Publications:
  1. Geng P, Sun J, Chen P, Brand E, Frame J, Meissner H, Stewart J, Gafner S, Clark S, Miller J, Harnly J. Characterization of Maca using a mass spectral fingerprinting, metabolomic analysis, and genetic sequencing approach. Planta Medica (in press).
  2. Harnly JM, Bergana MM, Adams KM, Xie Z, Moore JC. Variance of Commercial Powdered Milks Analyzed by 1H-3 NMR and Impact on Detection of Adulterants. J Agric Food Chem 66, 8478−8488 (2018). doi: 10.1021/acs.jafc.8b00432
  3. Harnly J. Importance of Accurate Measurements in Nutrition Research: Flavonoids. as a Case Study. Adv Nutr 7:375-382 (2016). doi: 10.3945/an.115.010470
  4. Harnly J, Chen P, Sun J, Huang H, Colson K, Yuk J, McCoy JA, Reynaud DH, Harrington P. Comparison of Flow Injection MS, NMR, and DNA Sequencing: Methods for Identification and Authentication of Black Cohosh (Actaea racemosa). J Planta Medica 81:1-13 (2015). doi: 10.1055/s-0035-1558113
  5. Balentine, D.A., Dwyer, J.T., Erdman, J.W., Harnly, J.M., Kwik-Urib, C.L. Recommendations on Reporting Requirements for Flavonoids in Research. Am J Clin Nutr. Doi: 10.3945ajcn.113.071274 (2015)
  6. Harnly, J.M., Harrington, P.B., Botros, L.L., Jablonski, J., Chang, C., Bergana, M.M., Wehling, P., Downey, G., Potts, A.R., Moore, J.C. Characterization of Near Infrared Spectral Variance in the Authentication of Skim and Nonfat Dry Milk Powder Collection Using ANOVA-PCA, Pooled-ANOVA, and Partial Least Squares Regression. J Ag Food Chem 62:0060-8067 (2014). doi: 10.1021/jf5013727
  7. Harnly, J.M., LaBudde, R. Probability of Identification (POI): a Statistical Model for the Validation of Qualitative Botanical Identification Methods. J. AOAC International 95:273-285 (2012).
  8. Luthria, D.L., Lin, L.-Z., Robbins, R.J., Finley, J.W., Banuelos, G.S. and Harnly, J.M. Discriminating between cultivars and treatments of broccoli using mass spectral fingerprinting and analysis of variance principal component analysis. J. Ag. Food Chem. 56:9819-9827 (2008). Doi: 10.1021/jf801606x
  9. Lin, L.-Z. and Harnly, J.M. A screening method for the identification of glycosylated flavonoids and other phenolic compounds using a standard analytical approach for all plant materials. J. Agric. Food Chem. 55:1084-1095 (2007). Doi: 10.1021/jf062431s
  10. Harnly, J.M., Doherty, R.F., Beecher, G.R., Holden, J.M., Haytowitz, D.B., Bhagwat, S. and Gebhardt, S. Flavonoid content of U.S. fruits, vegetables, and nuts. J. Agric. Food Chem. 54:9966-9977 (2006). Doi: 10.1021/jf061478a
      Dave Luthria Selected Publications:
  1. Nazrul, I, Bates, P.D., MariaJohn, K.M., Krishnan, H.B., Zhang, Z.Y. Luthria, D.L. Nataraja, S.S. Quantitative Proteomic Analysis of Low Linolenic Acid Transgenic Soybean Reveals Perturbations of Fatty Acid Metabolic Pathways. 2019,
  2. John, K.M.M., Harnly, J. M. and Luthria, D.L. Influence of direct and sequential extraction methodology on metabolic profiling. Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences, 1073:34-42. 2018,
  3. John, K.M.M., Bhagwat, A.A. and Luthria, D.L. Swarm motility inhibitory and antioxidant activities of pomegranate peel processed under three drying conditions. Food Chemistry 235:145-153. 2017,
  4. Ramakrishnan V., Ridge,C. D., Harnly M., Mazzola E. P., Luthria D. L. Spectroscopic analysis of wheat fractions and reconstituted whole wheat mixtures by 1H-NMR and NIR, Cereal Chem., 94:471-479. 2017,
  5. Luthria, D.L., Lu, Y., John, K.M.M. Bioactive phytochemicals in wheat: Extraction, analysis, processing, and functional properties. Journal of Functional Foods 18:910-925. 2015,
  6. Luthria, D. L. Optimization of extraction of phenolic acids from a vegetable waste product using a pressurized liquid extractor. J. Funct. Foods. 4 (4):842-850. 2012,
  7. Luthria, D. L., Mukhopadhyay, S., Lin, L. -Z., Harnly, J. M. A comparison of analytical and data preprocessing methods for spectral fingerprinting. Appl. Spectrosc. 65:250-259. 2011, DOI:10.1366/10-06109.
  8. Luthria D. L. and Vinyard B. T. Development of a Potential Reference Material for evaluating Antioxidant Activity. J. AOAC Int. 91:506-508. 2008.
  9. Luthria D.L. “Process for making an enriched mixture of polyunsaturated fatty acid methyl esters.” Patent # 6395778. Current patent rights are owned by Omega Tech, Inc.
  10. Luthria, D. L., Mohammed, B. S. and Sprecher, H. Regulation of the biosynthesis of 4,7,10,13,16,19-Docosahexaenoic acid. J. Biol. Chem. 271:16020-16025. 1996, DOI10.1074/jbc.271.27.16020.
      Craig Byrdwell

Dr. Byrdwell received his undergraduate and graduate degrees from the University of Louisville, writing his dissertation on identification of the ‘Unknown Phospholipid’ in the human eye lens, and quantification of fluorophores in normal and cataractous lenses. Dr. Byrdwell took a position at the USDA’s National Center for Agricultural Utilization Research, to work on analysis of triacylglycerols (TAGs) using HPLC with APCI-MS. Then, Dr. Byrdwell took a position at Florida Atlantic University, where he routinely employed dual mass spectrometers, in parallel, using both APCI-MS and ESI-MS. He re-joined ARS in 2005, and took on quantification of Vitamin D and TAGs. Recently, Dr. Byrdwell has been analyzing fat-soluble vitamins and TAGs using triple- and quadruple- parallel mass spectrometry approaches, combining three or four mass spectrometers employing complementary ionization methods (APCI-MS, APPI-MS, and ESI-MS) coupled to one, two, or three liquid chromatographs in LCx/MSy techniques. Dr. Byrdwell has published >60 peer-reviewed articles, 10 book chapters, and been Editor/Co-Editor of three AOCS Press books. He is on the editorial advisory board of Lipids, is the Lipidomics Associate Editor for The Lipid Library ( Dr. Byrdwell received the 2012 American Oil Chemists’ Society (AOCS) Analytical Division Herbert J. Dutton Award, presented the 2013 Society of Chemical Industry Julius Lewkowitsch Award Lecture in Ghent, Belgium, and in May 2019 received the Fellow of the AOCS Award.

      Pei Chen

Dr. Chen received his B.S. in Biology from the Peking (Beijing) University in China and his Ph.D. in Pharmaceutics from the University of Florida. Following a postdoctoral position at the George Washington University, he worked as a LC/MS specialist in Thermo Scientific in 1998, and at LionBiosciences and Diversa Co. between 1999 and 2004. He accepted a permanent position at the Food Composition and Methods Development Laboratory with USDA, ARS in 2004 and has been working there as a Research Chemist. Dr. Chen’s current research interests involve development of new LC/MS methodology for identification and quantitation of nutrients and bio-active compounds foods and dietary supplements. He is especially interested in metobolomic research involving plant materials and developing fingerprint/chemometric methodologies to assess herbal supplements and/or food materials.

      James Harnly

James Harnly, PhD, is an analytical chemist with expertise in atomic and molecular spectroscopy and authentication of food and botanical materials using chemometric methods. He has more than 40 years of experience in industry and government. He received his Bachelor’s degree from Colorado University and his Ph.D. from the University of Maryland. He has served as the Research Leader for the Food Composition and Methods Development Laboratory at the Beltsville Human Nutrition Research Center (Agricultural Research Service, US Department of Agriculture) since 1997. He now serves as the Research Leader for the newly organized Methods and Applications Food Composition Lab, where he is responsible for FoodData Central, the new USDA food composition database system, and the analytical support group. Dr. Harnly has authored more than 150 peer-reviewed papers, 18 technical reports and book chapters, and holds two patents. He served as the US editor of the Journal of Analytical Atomic Spectrometry for 22 years, as Editor-in-Chief of the Journal of Food composition and Analysis. He is a member of the Society for Applied Spectroscopy, American Society for Nutrition, American Society for Mass Spectrometry, and AOAC International. He served on the Board of Directors for AOAC International and is on the Advisory Board for the American Botanical Council.

      Dave Luthria

Dr. Luthria has over 25 years of experience conducting research on various projects in agriculture, food, and nutrition. He has authored or coauthored around100 peer-reviewed publications one patent discovery, one patent application, and seven book chapters. He has edited a book entitled “Oil extraction and analysis: critical issues and comparative studies” published by AOCS Press 2004. As a postdoctoral associate at The Ohio State University, he performed research on synthesis, structural elucidation, and metabolism of polyunsaturated fatty acids (PUFAs) where he discovered three novel biochemical pathways for metabolism of PUFAs. At UC Davis he was involved with the development of analytical methods for polyphenols from wine and biological matrices. At Monsanto, he developed high throughput extraction and analysis methods for the food library program and grain analysis. He played a crucial role in ISO17025 Certification of the Crop Analytics Laboratory in Ankeny, Iowa, where he served as a site lead for around three years. He serves on editorial board of multiple peer-reviewed scientific journals. He has mentored over 50 students from high school to postdoctoral fellows from diverse international backgrounds. He has served as a Fulbright Research Scholar and has completed two leadership programs (Key Executive Leadership Certificate Program and Executive Potential Program) at USDA and Executive Masters in International Business from St. Louis University. He has presented his research at multiple international and national conferences in over ten countries. He has been a member of different professional societies.