Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry |
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| Affiliation: | 1. College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Republic of Korea;2. Department of Pharmacognosy and Research Institute of Pharmaceutical Sciences, School of Pharmacy, The University of Mississippi, University, MS 38677, USA;3. College of Pharmacy, CMRI, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701 and 700-422, Republic of Korea;4. BK21 Plus KNU Biomedical Convergence Program, Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 702-701 and 700-422, Republic of Korea;5. College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea;6. National Center for Natural Products Research, The University of Mississippi, University, MS 38677, USA;1. Gyeonggi Institute of Science & Technology Promotion Natural Products Research Institute, Suwon 443-766, Republic of Korea;2. College of Pharmacy, Dankook University, Cheonan 330-714, Republic of Korea;3. Department of Biology, Duke University, Durham, NC 27708, USA |
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| Abstract: | Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products. |
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| Keywords: | Natural products Dereplication Tandem mass spectra Seven Golden Rules MS-FINDER |
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