Data-Based Chemical Class Regions for Van Krevelen Diagrams

Abstract

Ultrahigh resolution mass spectrometry (UHR-MS) is commonly used to characterize natural organic matter (NOM). The complexity of both NOM and the data set produced make data visualization challenging. Van Krevelen diagramsplots of component hydrogen/carbon (H/C) against oxygen/carbon (O/ C) elemental ratioshave become a popular way to visualize the chemical formulas identified by UHR-MS. Different regions on the van Krevelen diagram have been attributed to different chemical classes; however, the classifications vary between studies and the regions lack standard definitions. Here, chemical formulas were obtained from public databases to create H/C and O/C ranges for amino sugar, carbohydrate, lignin, lipid, peptide, and tannin chemical classes on van Krevelen diagrams. The recommended H/ C and O/C ranges are presented in a table and can be adapted to any data analysis software programs. The regions recommended here agreed reasonably well with previous literature for amino sugar, carbohydrate, lignin, lipid, and peptide regions. However, the recommended tannin region appears at lower H/C ratio values and with a wider range of O/C ratio values compared to previous studies. The regions presented herein are strongly recommended for use as consistent reference points in future NOM characterization studies to aid in the discussion of data and to readily compare studies.

Mass difference matching unfolds hidden molecular structures of dissolved organic matter

“…We chose the structural domains reprinted in the 2014 review by Minor et al for reference, because this represents the general level of detail and type of classes distinguished in recent DOM studies (Figure S-4). 57,58,[68][69][70] In two separate analyses, formulas were also classified with a more general and a data-based Van Krevelen scheme besides the reference one. 58,71 Finally, we assessed the agreement between structures predicted by Δm matching and those suggested in natural product structural databases.…”

“…57,58,[68][69][70] In two separate analyses, formulas were also classified with a more general and a data-based Van Krevelen scheme besides the reference one. 58,71 Finally, we assessed the agreement between structures predicted by Δm matching and those suggested in natural product structural databases. We combined structure suggestions from different databases, including Dictionary of Natural Products 72 , KNApSAcK 73 , Metacyc 74 , KEGG 75 , and HMDB 76 as well as their expanded in-silico annotations based on predicted enzymatic transformations in the MINEs database.…”

“…All in all, our results show that it may be possible to refine molecular structure representations in Van Krevelen plots by deconvoluted MS 2 data, and that complementary precursor ion information could be used to assess false or biased Δm-based class assignments (e.g., elemental composition, DBE, ionization, fragmentation sensitivity, ion mobility, polarity index, etc.). 13,55,58 Fluorescence or NMR spectroscopy could add valuable information if DOM would be fractionated before MS 2 data acquisition, i.e., to assess indirect (statistical) links of MS 2 features with complementary forms of structural insight. 21,[94][95][96] Our findings must however be taken with caution for four reasons:…”

“…Lastly, we hypothesized that indicative Δm features of plant phenols, e.g., lignin-and tannin-related losses, would match their yet unknown structural analogs in DOM and that these patterns would reflect commonly applied "structural domain" distributions. 55,57,58…”

Probing the impact of a phytoplankton bloom on the chemistry of nascent sea spray aerosol using high-resolution mass spectrometry

“…Although a large amount of fresh organic carbon is produced by photosynthesizing microorganisms most of this organic matter is rapidly consumed and modified so that DOM represents a mixture of different forms of labile and recalcitrant compounds [98]. By visualising the complex nature of DOM mass spectra using van Krevelen diagrams it is possible to assign certain regions of the diagram to a specific class of compounds [82,99,100]. The majority of the molecular formulas present in the most polar fraction A and a significant part of molecular formulas from polarity fraction B fall in the central part of the van Krevelen diagram that is attributed to carboxyl-rich alicyclic molecules (CRAM) [47,48].…”