Chemical Informatics Combined with Kendrick Mass Analysis to Enhance Annotation and Identify Pathways in Soybean Metabolomics
Year: 2025
Type: article
Abstract: Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels. Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress. Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exact m/z values are converted into Kendrick masses and their Kendrick mass defects (KMD) computed, which are then sorted from high to low KMD. This latter process assists in identifying many additional molecular formulas, and is noted to be particularly useful in identifying formulas whose mass difference corresponds to two hydrogen atoms. In this study, more than 460 ionic formulas are identified in Pana, and more than 340 ionic formulas are identified in PI 567731, with many of these formulas reported from soybean for the first time. Using the SoyCyc matches, the metabolic pathways from each cultivar are compared, providing for lists of molecular targets available to profile effects of abiotic stress on these soybean cultivars. Key metabolites include chlorophylls, pheophytins, mono- and diacylglycerols, cycloeucalenone, squalene, and plastoquinones and involve pathways which include the anabolism and catabolism of chlorophyll, glycolipid desaturation, and biosynthesis of phytosterols, plant sterols, and carotenoids.
Source: Metabolites
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,258
OpenAlex ID: W4406804810