Discovering Nature's Fingerprints: Isotope Ratio Analysis on Bioanalytical Mass Spectrometers

Advancing Stable Isotope Analysis with Orbitrap-MS for Fatty Acid Methyl Esters and Complex Lipid Matrices

Isotopic analysis plays a crucial role in different scientific fields, offering valuable insights that aid in elucidating biosynthetic pathways, determining geographic origin, and identifying product adulteration. Established mass spectrometry techniques for isotopic analysis require the conversion of samples into gases prior to introduction into the systems. Moreover, the ionization process in these methods is destructive, potentially leading to the loss of essential molecular structure information. Thus, alternative analytical methods, such as Orbitrap-MS, could be a useful tool to determine stable isotope ratios. This paper describes an Orbitrap-based method using stearic acid methyl ester as a model molecule to determine the stable isotopic ratios of fatty acids and fatty acid methyl esters (FAMEs) in different vegetable butters. Orbitrap analyses were performed in positive ionization mode with both [M + H]+ and [M + Na]+ ions considered for the analysis. Nine standards (Std 1-Std 9) and three vegetable butters (cupuaçu, cocoa, and shea) were employed in the study. The standards were employed to develop the method and were measured using HPLC and a dual-inlet system. Both injections achieved high precision (<1.5‰) when compared with the IRMS data; however, the HPLC showed the most accuracy and was selected for direct injection measurement of the natural samples. Our results demonstrated the efficiency of the ESI-Orbitrap system in differentiating sources based on δ13C values. This study not only advances the use of high-resolution mass spectrometry for isotope analysis but also opens new avenues for applying stable isotopes in food sciences.

Is Photosynthesis-Derived NADPH Really a Source of 2H-Depleted Hydrogen in Plant Compounds?

We provide evidence that photosynthetically produced NADPH is not the major source of 2H‐depletion in carbohydrates.

Isotope Techniques in Chemical Wastewater Treatment: Opportunities and Uncertainties

A comprehensive and in-depth analysis of reaction mechanisms is essential for advancing chemical water treatment technologies. However, due to the limitations of conventional experimental and analytical methods, the types of reactive species and their generation pathways are commonly debatable in many aqueous systems. As highly sensitive diagnostic tools, isotope techniques offer deeper insights with minimal interference from reaction conditions. Nevertheless, precise interpretations of isotope results remain a significant challenge. Herein, we first scrutinized the fundamentals of isotope chemistry and highlighted key changes induced by the isotope substitution. Next, we discussed the application of isotope techniques in kinetic isotope effects, presenting a roadmap for interpreting KIE in sophisticated systems. Furthermore, we summarized the applications of isotope techniques in elemental tracing to pinpoint reaction sites and identify dominant reactive species. Lastly, we propose future research directions, highlighting critical considerations for the rational design and interpretation of isotope experiments in environmental chemistry and related fields.

Shining a new light on the classical concepts of carbon-isotope dendrochronology

Retrospective information about plant ecophysiology and the climate system are key inputs in Earth system and vegetation models. Dendrochronology provides such information with large spatiotemporal coverage, and carbon-isotope analysis across tree-ring series is among the most advanced dendrochronological tools. For the past 70 years, this analysis was performed on whole molecules and, to this day, 13C discrimination during carbon assimilation is invoked to explain isotope variation and associated climate signals. However, recently it was reported that tree-ring glucose exhibits multiple isotope signals at the intramolecular level (see Wieloch et al., 2025). Here, I estimated the signals' contribution to whole-molecule isotope variation and found that downstream processes in leaf and stem metabolism each introduce more variation than carbon assimilation. Moreover, downstream processes introduce most of the climate information. These findings are inconsistent with the classical concepts/practices of carbon-isotope dendrochronology. More importantly, intramolecular tree-ring isotope analysis promises novel insights into forest metabolism and the climate of the past.

Reconciling water-use efficiency estimates from carbon isotope discrimination of leaf biomass and tree rings: nonphotosynthetic fractionation matters

Carbon isotope discrimination (∆) in leaf biomass (∆BL) and tree rings (∆TR) provides important proxies for plant responses to climate change, specifically in terms of intrinsic water-use efficiency (iWUE). However, the nonphotosynthetic 12C/13C fractionation in plant tissues has rarely been quantified and its influence on iWUE estimation remains uncertain. We derived a comprehensive, ∆ based iWUE model (iWUEcom) which includes nonphotosynthetic fractionations (d) and characterized tissue-specific d-values based on global compilations of data of ∆BL, ∆TR and real-time ∆ in leaf photosynthesis (∆online). iWUEcom was further validated with independent datasets. ∆BL was larger than ∆online by 2.53‰, while ∆BL and ∆TR showed a mean offset of 2.76‰, indicating that ∆TR is quantitatively very similar to ∆online. Applying the tissue-specific d-values (dBL = 2.5‰, dTR = 0‰), iWUE estimated from ∆BL aligned well with those estimated from ∆TR or gas exchange. ∆BL and ∆TR showed a consistent iWUE trend with an average CO2 sensitivity of 0.15 ppm ppm-1 during 1975-2015. Accounting for nonphotosynthetic fractionations improves the estimation of iWUE based on isotope records in leaf biomass and tree rings, which is ultimate for inferring changes in carbon and water cycles under historical and future climate.

The marriage between stable isotope ecology and plant metabolomics - new perspectives for metabolic flux analysis and the interpretation of ecological archives

Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment-metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.

Position-Specific Oxygen Isotope Analysis in Inositol Phosphates by Using Electrospray Ionization-Quadrupole-Orbitrap Mass Spectrometry

Conventional isotope-ratio mass spectrometry measurements obscure position-specific isotope distributions in molecular compounds because these measurements require an initial step that converts compounds into simple gases by combustion or pyrolysis. Here, we used electrospray ionization (ESI)-based Orbitrap mass spectrometry to measure oxygen isotope ratios in the phosphate and hydroxyl moieties of inositol phosphates. A thermal hydrolysis experiment was conducted using 18O-labeled water to examine the position-specific oxygen isotope exchange in inositol hexakisphosphate (IP6) as well as its hydrolysis products IP5, IP3, and PO3 fragments. Measurement precisions of the position-specific and molecular-average oxygen isotope values of inositol phosphates were better than ±1.1‰ and ±0.5‰, respectively. Under optimized ionization and Orbitrap parameters, this level of precision was obtained within 30 min of run time at 60 μM initial concentration of inositol phosphate. The ability to measure phosphate-specific oxygen isotopes in inositol phosphate enabled the quantification of isotope exchange, which did not occur in phosphate on IP6, IP5, IP3, and PO3 fragments, meaning that the change in isotopes should have resulted from hydroxyls in the ring. Isotope mass balance calculations corroborated that hydroxyl oxygens are derived from 18O-labeled water. With the observed sensitivity and precision achieved in this study, Orbitrap IRMS proved to be a promising tool for investigating the position-specific oxygen isotopes in organophosphorus compounds. These outcomes open up numerous potential applications that can expand our understanding of phosphorus cycling in the environment.

A guide to precise measurements of isotope abundance by ESI-Orbitrap MS

Stable isotopes of carbon, hydrogen, nitrogen, oxygen and sulfur are widespread in nature. Nevertheless, their relative abundance is not the same everywhere. This is due to kinetic isotope effects in enzymes and other physical principles such as equilibrium thermodynamics. Variations in isotope ratios offer unique insights into environmental pollution, trophic relationships in ecology, metabolic disorders and Earth history including climate history. Although classical isotope ratio mass spectrometry (IRMS) techniques still struggle to access intramolecular information like site-specific isotope abundance, electrospray ionization-Orbitrap mass spectrometry can be used to achieve precise and accurate intramolecular quantification of isotopically substituted molecules ('isotopocules'). This protocol describes two procedures. In the first one, we provide a step-by-step beginner's guide for performing multi-elemental, intramolecular and site-specific stable isotope analysis in unlabeled polar solutes by direct infusion. Using a widely available calibration solution, isotopocules of trifluoroacetic acid and immonium ions from the model peptide MRFA are quantified. In the second approach, nitrate is used as a simple model for a flow injection routine that enables access to a diverse range of naturally occurring isotopic signatures in inorganic oxyanions. Each procedure takes 2-3 h to complete and requires expertise only in general mass spectrometry. The workflows use optimized Orbitrap IRMS data-extraction and -processing software and are transferable to various analytes amenable to soft ionization, including metabolites, peptides, drugs and environmental pollutants. Optimized mass spectrometry systems will enable intramolecular isotope research in many areas of biology.

Quartz Crystal Microbalance as a Holistic Detector for Quantifying Complex Organic Matrices during Liquid Chromatography: 2. Compound-Specific Isotope Analysis

In carbon-compound-specific isotope analysis (carbon CSIA) of environmental micropollutants, purification of samples is often required to guarantee accurate measurements of a target compound. A companion paper has brought forward an innovative approach to couple a quartz crystal microbalance (QCM) with high-performance liquid chromatography (HPLC) for the online quantification of matrices during a gradient HPLC purification. This work investigates the benefit for isotope analysis of polar micropollutants typically present in environmental samples. Here, we studied the impact of the natural organic matter (NOM) on the isotopic integrity of model analytes and the suitability of the NOM-to-analyte ratio as a proxy for the sample purity. We further investigated limitations and enhancement of HPLC purification using QCM on C18 and C8 phases for single and multiple targets. Strong isotopic shifts of up to 3.3% toward the isotopic signature of NOM were observed for samples with an NOM-to-analyte ratio ≥10. Thanks to QCM, optimization of matrix removal of up to 99.8% of NOM was possible for late-eluting compounds. The efficiency of HPLC purification deteriorated when aiming for simultaneous purification of two or three compounds, leading to up to 2.5% less NOM removal. Our results suggest that one optimized HPLC purification can be achieved through systematic screening of 3 to 5 different gradients, thereby leading to a shift of the boundaries of accurate carbon CSIA by up to 2 orders of magnitude toward lower micropollutant concentrations.

Why leaves become isotopically lighter than photosynthetic carbon isotope discrimination explains: on the importance of post-photosynthetic fractionation

This article comments on:

Yu YZ, Liu HT, Yang F, Li L, Schäufele R, Tcherkez G, Schnyder H, Gong XY. 2024. δ13C of bulk organic matter and cellulose reveal post-photosynthetic fractionation during ontogeny in C4 grass leaves. Journal of Experimental Botany 75, 1451–1464

Natural Abundance Isotope Ratio Measurements of Organic Molecules Using 21 T FTICR MS

Subtle variations in stable isotope ratios at natural abundance are challenging to measure but can yield critical insights into biological, physical, and geochemical processes. Well-established methods, particularly multicollector, gas-source, or plasma isotope ratio mass spectrometry, are the gold standard for stable isotope measurement, but inherent limitations in these approaches make them ill-suited to determining site-specific and multiply substituted isotopic abundances of all but a few compounds or to characterizing larger intact molecules. Fourier transform mass spectrometry, namely, Orbitrap mass spectrometry, has recently demonstrated the ability to measure natural abundance isotope ratios with chemically informative accuracy and precision. Here, we report the first use of Fourier transform ion cyclotron resonance mass spectrometry for the accurate (<1‰) and precise (<1‰ standard error) simultaneous determination of δ13C and δ15N in caffeine isotopologues and provide a discussion of the critical instrumental parameters necessary to make such measurements. We further report the ability to make these measurements with online liquid chromatography, expanding the ability of this technique to explore mixtures in the future.

Assessment of stable carbon isotope 13С/12С ratio in phthalates from surface waters using HPLC-HRMS-TOF approach

A method for estimating the ratio of stable carbon isotopes 13С/12С in the composition of phthalates from surface water at a trace concentration level is proposed. It is based on the concentration of hydrophobic components of water using an analytical reversed phase HPLC column followed by their gradient separation and detection of eluted phthalates using a high-resolution time-of-flight mass spectrometer (ESI-HRMS-TOF) in the form of molecular ions. The ratio of stable carbon isotopes 13С/12C in phthalates is calculated as a ratio of integrals under the monoisotopic [M+1+H]+ and [M+H]+ peaks. The Δ13C value is calculated relatively to the 13C/12C ratio in commercial DnBP and DEHP phthalates used as standards. The minimal concentration of DnBP and DEHP in water required for a reliable determination of Δ13C value is estimated by the level of ca. 0.2 μg L-1. The technique has been verified during the monitoring of priority phthalates in the waters of Lake Baikal.