Assay Publications

Advancing metabolomics through innovative assay development and validation

NMR

Automated beer analysis by NMR spectroscopy.
Lee, B. L., Shahin, F., Selim, A., Berjanskii, M., Torres-Calzada, C., Kovur, P., Mandal, R., & Wishart, D. S. (2025). Automated beer analysis by NMR spectroscopy. ACS Food Sci. Technol. 5(1): 378–388.

Accurate prediction of 1H NMR chemical shifts of small molecules using machine learning.
Sajed, T., Sayeeda, Z., Lee, B.L., Berjanskii, M., Wang, F., Gautam, V. and Wishart, D.S. (2024) Accurate prediction of 1H NMR chemical shifts of small molecules using machine learning. Metabolites, 14(5): 290.
Automatic chemical profiling of wine by proton nuclear magnetic resonance spectroscopy.
Lee, B.L., Rout, M., Dong, Y., Lipfert, M., Berjanskii, M., Shahin, F., Bhattacharyya, D., Selim, A., Mandal, R. and Wishart, D.S. (2024) Automatic chemical profiling of wine by proton nuclear magnetic resonance spectroscopy. ACS Food Sci. Technol. 4(8):1937-1949.

Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy.
Lee, B.L., Rout, M., Mandal, R. and Wishart, D.S. (2023). Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy. Magn. Reson. Chem. 61(12):705-717.
A data deposition platform for sharing nuclear magnetic resonance data.
Pin, M., Poynton, E.F., Jordan, T., Kim, J., Ledingham, B., van Santen, J.A., Yang, V., Maras, A., Tavangar, P., Gautam, V., Peters, H., Sajed, P., Lee, B., Shreffler, H. A., Koller, J. T., Tretter, Z. M., Cort, J. R., Sumner, L. W., Wishart, D. S. and Linington, R. G. (2023). A data deposition platform for sharing nuclear magnetic resonance data. J. Nat. Prod. 86(11): 2554-2561..
Best practices in NMR metabolomics: Current state.
Schock, T., Bayless, A., Gouveia, G., Powers, R., Copie, V., Cort, J., Eghbalnia, H.R., Pathmasiri, W., Wishart, D.S., Andersson, E., Brua, R., Cheng, L., Clendinen, C., Cochran, D., Crook, A., Jeppesen, M., Maroli, A., Merritt, M., Roth, H., Sakalliouglu, I., Sarma, S., Sumner, L., Takis, P. and Uchimiya, M. (2023). Best practices in NMR metabolomics: Current state. TrAC Trends Anal Chem. 171:117478.
Securing the Future of NMR Metabolomics Reproducibility: A Call for Standardized Reporting.
Andersson, E. R., Bayless, A. L., Brua, R. B., Casu, F., Cheng, L. L., Choo, M., Edison, A. S., Eghbalnia, H. R., Fleischer, C. C., Gouveia, G. J., Hoch, J. C., Kaur, G., Li, D. W., Pathmasiri, W., Pelczer, I., Probert, F., Raftery, D., Rovnyak, D., Secreto, M., Schock, T. B., … Gebregiworgis, T. (2025). Securing the Future of NMR Metabolomics Reproducibility: A Call for Standardized Reporting. Analytical chemistry, 97(38), 20655–20666.

NMR and metabolomics- A roadmap for the future.
Wishart, D.S., Cheng, L.L., Copié, V., Edison, A.S., Eghbalnia, H.R., Hoch, J.C., Gouveia, G.J., Pathmasiri, W., Powers, R., Schock, T.B., Sumner, L.W. and Uchimiya, M. (2022) NMR and metabolomics- A roadmap for the future. Metabolites, 12(8): 678.
“Practical Aspects of NMR-Based Metabolomics” in Metabolomics and Its Impact on Health and Diseases
Wishart, D.S., Rout, M., Lee, B.L., Berjanskii, M., LeVatte, M. and Lipfert, M. (2022). “Practical Aspects of NMR-Based Metabolomics” in Metabolomics and Its Impact on Health and Diseases (Eds. Ghini, V., Stringer, K.A., Luchinat, C.), Springer, Cham., pp. 1-41.

Software Development

A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer.
Bhattacharyya, D., LeVatte, M. A., Singh, U., Issac, F., Karim, M., Ali, S., Sieben, A., Huang, S., and Wishart, D. S. (2024). A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer. Anal. Biochem. 697: 115717.
A fully automated web server for targeted nuclear magnetic resonance metabolomics of plasma and serum.
Rout M, Lipfert M, Lee BL, Berjanskii M, Assempour N, Fresno RV, Cayuela AS, Dong Y, Johnson M, Shahin H, Gautam V, Sajed T, Oler E, Peters H, Mandal R, Wishart DS. MagMet: Magn Reson Chem. 2023 Dec;61(12):681-704. doi: 10.1002/mrc.5371. Epub 2023 Jun 2. PMID: 37265034.

Software Validation

Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy.
Lee BL, Rout M, Mandal R, Wishart DS. Magn Reson Chem. 2023 Dec;61(12):705-717. doi: 10.1002/mrc.5372. Epub 2023 Jun 2. PMID: 37265043.

PRIME

Neonatal and Pediatric Health

The Childhood Acute Illness and Nutrition (CHAIN) network nested case-cohort study protocol: a multi-omics approach to understanding mortality among children in sub-Saharan Africa and South Asia.
Njunge JM, Tickell K, Diallo AH, Sayeem Bin Shahid ASM, Gazi MA, Saleem A, Kazi Z, Ali S, Tigoi C, Mupere E, Lancioni CL, Yoshioka E, Chisti MJ, Mburu M, Ngari M, Ngao N, Gichuki B, Omer E, Gumbi W, Singa B, Bandsma R, Ahmed T, Voskuijl W, Williams TN, Macharia A, Makale J, Mitchel A, Williams J, Gogain J, Janjic N, Mandal R, Wishart DS, Wu H, Xia L, Routledge M, Gong YY, Espinosa C, Aghaeepour N, Liu J, Houpt E, Lawley TD, Browne H, Shao Y, Rwigi D, Kariuki K, Kaburu T, Uhlig HH, Gartner L, Jones K, Koulman A, Walson J, Berkley J. Gates Open Res. 2022 Nov 3;6:77. doi: 10.12688/gatesopenres.13635.2. PMID: 36415883; PMCID: PMC9646488.
The Urinary Metabolome of Healthy Newborns.
López-Hernández Y, Oropeza-Valdez JJ, Blanco-Sandate JO, Herrera-Van Oostdam AS, Zheng J, Chi Guo A, Lima-Rogel V, Rajabzadeh R, Salgado-Bustamante M, Adrian-Lopez J, Castillo CG, Robles Arguelles E, Monárrez-Espino J, Mandal R, Wishart DS. Metabolites. 2020 Apr 23;10(4):165. doi: 10.3390/metabo10040165. PMID: 32340350; PMCID: PMC7240964.
Urinary Metabolomic Profile of Neonates Born to Women with Gestational Diabetes Mellitus.
Herrera-Van Oostdam AS, Salgado-Bustamante M, Lima-Rogel V, Oropeza-Valdez JJ, López JA, Rodríguez IDR, Toro-Ortiz JC, Herrera-Van Oostdam DA, López-Hernández Y, Monárrez-Espino J. Metabolites. 2021 Oct 22;11(11):723. doi: 10.3390/metabo11110723. PMID: 34822382; PMCID: PMC8621167.
Systemic inflammation and metabolic disturbances underlie inpatient mortality among ill children with severe malnutrition.
Wen B, Njunge JM, Bourdon C, Gonzales GB, Gichuki BM, Lee D, Wishart DS, Ngari M, Chimwezi E, Thitiri J, Mwalekwa L, Voskuijl W, Berkley JA, Bandsma RH. Sci Adv. 2022 Feb 18;8(7):eabj6779. doi: 10.1126/sciadv.abj6779. Epub 2022 Feb 16. PMID: 35171682; PMCID: PMC8849276.
A164 IDENTIFYING THE MOST IMPORTANT PREDICTORS TO CORRELATE SERUM METABOLITES WITH MRE CHANGES IN PATIENTS WITH PEDIATRIC CROHN DISEASE.
R G Suarez, N Guruprasad, G Tata, Z Zhang, G Focht, V Navas-López, S Koletzko, A M Griffiths, D Wishart, E Wine, Journal of the Canadian Association of Gastroenterology, Volume 6, Issue Supplement_1, March 2023, Pages 10–11, https://doi.org/10.1093/jcag/gwac036.164

Plants

A Comprehensive Targeted Metabolomics Assay for Crop Plant Sample Analysis.
Zheng, J.; Johnson, M.; Mandal, R.; Wishart, D.S. Metabolites 2021, 11, 303. https://doi.org/10.3390/metabo11050303

Others

A comprehensive LC–MS metabolomics assay for quantitative analysis of serum and plasma.
Zhang, L., Zheng, J., Johnson, M., Mandal, R., Cruz, M., Martínez-Huélamo, M., Andres-Lacueva, C., and Wishart, D. S. (2024). A comprehensive LC–MS metabolomics assay for quantitative analysis of serum and plasma. Metabolites14(11): 622.
Predictive blood biomarkers of sheep pregnancy and litter size.
Goldansaz SA, Markus S, Plastow G, Wishart DS. Sci Rep. 2022 Jun 20;12(1):10307. doi: 10.1038/s41598-022-14141-w. PMID: 35725997; PMCID: PMC9209467.
Blood Metabolomic Phenotyping of Dry Cows Could Predict the High Milk Somatic Cells in Early Lactation—Preliminary Results.
Haxhiaj, K.; Li, Z.; Johnson, M.; Dunn, S.M.; Wishart, D.S.; Ametaj, B.N. Dairy 2022, 3, 59-77. https://doi.org/10.3390/dairy3010005

GC-MS

Accurate prediction of isothermal gas chromatographic kováts retention indices.
Anjum, A., Liigand, J., Milford, R., Gautam, V. and Wishart, D.S. (2023). Accurate prediction of isothermal gas chromatographic kováts retention indices. J. Chromatogr. A 1705:464176.

LC-MS

A comprehensive LC–MS metabolomics assay for quantitative analysis of serum and plasma.
Zhang, L., Zheng, J., Johnson, M., Mandal, R., Cruz, M., Martínez-Huélamo, M., Andres-Lacueva, C., and Wishart, D. S. (2024). A comprehensive LC–MS metabolomics assay for quantitative analysis of serum and plasma. Metabolites 14(11): 622.

MS-MS

A spectroscopic test suggests that fragment ion structure annotations in MS/MS libraries are frequently incorrect.
van Tetering, L., Spies, S., Wildeman, Q.D., Houthuijs, K.J., van Outersterp, R.E., Martens, J., Wevers, R.A., Wishart, D.S., Berden, G. and Oomens, J. (2024). A spectroscopic test suggests that fragment ion structure annotations in MS/MS libraries are frequently incorrect. Commun. Chem. 7(1): 30.

General metabolomics

2025

Recommendations for sample selection, collection and preparation for NMR-based metabolomics studies of blood.
Emwas, A. H., Zacharias, H. U., Alborghetti, M. R., Gowda, G. A. N., Raftery, D., McKay, R. T., Chang, C. K., Saccenti, E., Gronwald, W., Schuchardt, S., Leiminger, R., Merzaban, J., Madhoun, N. Y., Iqbal, M., Alsiary, R. A., Shivapurkar, R., Pain, A., Shanmugam, D., Ryan, D., Roy, R., … Wishart, D. S. (2025). Recommendations for sample selection, collection and preparation for NMR-based metabolomics studies of blood. Metabolomics : Official journal of the Metabolomic Society, 21(3), 66.
Quantitative comparison of whole blood, plasma and serum metabolomes across different blood collection methods.
Zubkowski, A., López-Hernández, Y., Rayat, D. Y., Zheng, J., Hiebert-Giesbrecht, M. R., Johnson, M., Kovur, P., Mandal, R., & Wishart, D. S. (2025). Quantitative comparison of whole blood, plasma and serum metabolomes across different blood collection methods. Metabolomics : Official journal of the Metabolomic Society, 21(5), 146.
Comprehensive and quantitative urinary metabolomic profiling for improved characterization of diabetic nephropathy.
López-Hernández, Y., Oropeza-Valdez, J. J., Maeda-Gutiérrez, V., Zheng, J., Mandal, R., López-Ramos, J. E., Moreira Hernández, J. C., Jaime-Sánchez, E., Romo-García, M. F., Enciso Moreno, J. A., & Wishart, D. S. (2025). Comprehensive and quantitative urinary metabolomic profiling for improved characterization of diabetic nephropathy. Metabolomics : Official journal of the Metabolomic Society, 21(6), 163.

2024

The Open SprayBot: A high-throughput paper spray mass spectrometry platform for disease screening.
García-Rojas, N.S., Guillén-Alonso, H., MacKay, S., Torres-Calzada, C., Soto-Rodriguez, L.D., Winkler, R. and Wishart, D.S. (2024) The Open SprayBot: A high-throughput paper spray mass spectrometry platform for disease screening. HardwareX, 19: e00551.
Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors.
Cruz, A. K., Alves, M. A., Andresson, T., Bayless, A. L., Bloodsworth, K. J., Bowden, J. A., Bullock, K., Burnet, M. C., Neto, F. C., Choy, A., Clish, C. B., Couvillion, S. P., Cumeras, R., Dailey, L., Dallmann, G., Davis, W. C., Deik, A. A., Dickens, A. M., Djukovic, D., … da Silva, S. (2024). Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors. Metabolomics 20(6): 125.
An overview of pre-analytical factors impacting metabolomics analyses of blood samples.
Thachil, A., Wang, L., Mandal, R., Wishart, D. and Blydt-Hansen, T. (2024) An overview of pre-analytical factors impacting metabolomics analyses of blood samples. Metabolites, 14(9): 474.
Chemical composition of commercial cannabis.
Wishart, D.S., Hiebert-Giesbrecht, M., Inchehborouni, G., Cao, X., Guo, A.C., LeVatte, M.A., Torres-Calzada, C., Gautam, V., Johnson, M., Liigand, J., Wang, F., Zahrei, S., Bhumireddy, S., Wang, Y., Zheng, J., Mandal, R. and Dyck, J. R. B. (2024). Chemical composition of commercial cannabis. J. Agric. Food Chem. 72(25):14099-14113.
A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer.
Bhattacharyya, D., LeVatte, M. A., Singh, U., Issac, F., Karim, M., Ali, S., Sieben, A., Huang, S., and Wishart, D. S. (2024). A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer. Anal. Biochem. 697: 115717.

2023

Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature.
Koistinen, V., Kärkkäinen, O., Keski-Rahkonen, P., Tsugawa, H., Scalbert, A., Arita, M., Wishart, D., Hanhineva, K. (2023) Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature. Nat. Metab. 5: 351–354.
Stability of nucleic acid bases in concentrated sulfuric acid: Implications for the habitability of Venus' clouds.
Seager, S., Petkowski, J.J., Seager, M.D., Grimes Jr, J.H., Zinsli, Z., Vollmer-Snarr, H.R., MK, A.E.R., Wishart, D.S., Lee, B.L., Gautam, V. and Herrington, L. (2023). Stability of nucleic acid bases in concentrated sulfuric acid: Implications for the habitability of Venus' clouds. PNAS 120(25): e2220007120.
A fast and accurate colorimetric assay for quantifying hippuric acid in human urine.
Bhattacharyya, D., LeVatte, M.A. and Wishart, D.S. (2023). A fast and accurate colorimetric assay for quantifying hippuric acid in human urine. Anal. Biochem. 680:115303.

2022

The Impact of methodological choices when developing predictive models using urinary metabolite data.
Krstic, N., Multani, K., Wishart, D.S., Blydt-Hansen, T. and Cohen Freue, G.V. (2022) The Impact of methodological choices when developing predictive models using urinary metabolite data. Stat. Med. 41(18): 3511-3526.

2021

A targeted serum metabolomics GC-MS approach identifies predictive blood biomarkers for retained placenta in Holstein dairy cows.
Zhang, G., Tobolski, D., Zwierzchowski, G., Mandal, R., Wishart, D.S. and Ametaj, B.N. (2021) A targeted serum metabolomics GC-MS approach identifies predictive blood biomarkers for retained placenta in Holstein dairy cows. Metabolites, 11(9):633.

Assay Publications

NMR

Software Development

Software Validation

PRIME

Neonatal and Pediatric Health

Plants

Others

GC-MS

LC-MS

MS-MS

General metabolomics

2025

2024

2023

2022

2021

Services

Research

Innovation

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