Application of Spectral Accuracy to Improve the Identification of Organic Compounds in Environmental Analysis

Machine-learning assisted molecular formula assignment to high-resolution mass spectrometry data of dissolved organic matter

High-resolution mass spectrometry (HRMS) provides molecular compositional information of dissolved organic matter (DOM) through isotopic assignment from the molecular mass. However, due to the inevitable deviation of molecular mass measurement and the limitation of resolving power, multiple possible solutions frequently occur for a given molecular mass. Lowering the mass deviation threshold and adding assignment restriction rules are often applied to exclude the incorrect solutions, which generally involves time-consuming manual post-processing of mass data. To improve the result accuracy in an automated manner, we developed a molecular formula assignment algorithm based on machine-learning technology. The method integrated a logistic regression model using manually corrected isotopic composition and the peak features of HRMS data (m/z, signal-to-noise ratio, isotope type, and number, etc.) as training data. The developed model can evaluate the correctness of a candidate formula for the given mass peak based on the peak features. The method was verified by various DOM samples FT-ICR MS data (direct infusion negative mode electrospray), achieving a ∼90% accuracy (compared to the traditional approach) for formula assignment. The method was applied to a series of NOM samples and showed a significant improvement in formula assignment compared with the mass matching method.

Uncovering transformation products of four organic contaminants of concern by photodegradation experiments and analysis of real samples from a local river

In this study, photodegradation experiments simulating the exposure conditions of sunlight on the commonly detected in surface and wastewater contaminants atorvastatin (ATV), bezafibrate (BEZ), oxybenzone (OXZ), and tris(2-butoxyethyl)phosphate (TBEP) were conducted as the fate of these compounds and their transformation products (TPs) was followed. Then a nontargeted analysis was carried out on an urban river to confirm the environmental occurrence of the TPs after which the ECOSAR software was used to generate predicted effect levels of toxicity of the detected TPs on aquatic organisms. Five TPs of ATV were tentatively identified including two stable ones at the end of the experiment: ATV_TP557a and ATV_TP575, that were the product of hydroxylation. Complete degradation of OXZ was observed in the experiment with no significant TP identified. BEZ remained stable and largely undegraded at the end of the exposure. Five TPs of TBEP were found including four that were stable at the end of the experiment: TBEP_TP413, TBEP_TP415, TBEP_TP429, and TBEP_TP343. In the nontargeted analysis, ATV_TP557b, a positional isomer of ATV_TP557a, ATV_TP575 and the 5 TPs of TBEP were tentatively identified. The predicted concentration for effect levels were lower for ATV_TP557b compared to ATV indicating the TP is potentially more toxic than the parent compound. All the TPs of TBEP showed lower predicted toxicity toward aquatic organisms than their parent compound. These results highlight the importance of conducting complete workflows from laboratory experiments, followed by nontargeted analysis to confirm environmental occurrence to end with predicted toxicity to better communicate concern of the newfound TPs to monitoring programs.

Non-targeted screening of trace organic contaminants in surface waters by a multi-tool approach based on combinatorial analysis of tandem mass spectra and open access databases

Non-targeted screening (NTS) in mass spectrometry (MS) helps alleviate the shortcoming of targeted analysis such as missing the presence of concerning compounds that are not monitored and its lack of retrospective analysis to subsequently look for new contaminants. Most NTS workflows include high resolution tandem mass spectrometry (HRMS²) and structure annotation with libraries which are still limited. However, in silico combinatorial fragmentation tools that simulate MS² spectra are available to help close the gap of missing compounds in empirical libraries. Three NTS tools were combined and used to detect and identify unknown contaminants at ultra-trace levels in surface waters in real samples in this qualitative study. Two of them were based on combinatorial fragmentation databases, MetFrag and the Similar Partition Searching algorithm (SPS), and the third, the Global Natural Products Social Networking (GNPS), was an ensemble of empirical databases. The three NTS tools were applied to the analysis of real samples from a local river. A total of 253 contaminants were identified by combining all three tools: 209 were assigned a probable structure and 44 were confirmed using reference standards. The two major classes of contaminants observed were pharmaceuticals and consumer product additives. Among the confirmed compounds, octylphenol ethoxylates, denatonium, irbesartan and telmisartan are reported for the first time in surface waters in Canada. The workflow presented in this work uses three highly complementary NTS tools and it is a powerful approach to help identify and strategically select contaminants and their transformation products for subsequent targeted analysis and uncover new trends in surface water contamination.

Non-target environmental analysis by liquid chromatography/high-resolution mass spectrometry with a product ion and neutral loss database

Despite the increasing detection of emerging substances in the environment, the identity of most are left unknown due to the lack of efficient identification methods. We developed a non-target analysis method for identifying unknown substances in the environment by liquid chromatography/high-resolution mass spectrometry (LC/HRMS) with a product ion and neutral loss database (PNDB). The present analysis describes an elucidation method with elemental compositions of the molecules, product ions, and corresponding neutral losses of the unknown substance: (1) with the molecular formula, possible molecular structures are retrieved from two chemical structure databases (PubChem and ChemSpider); then (2) with the elemental compositions of product ions and neutral losses, possible partial structures are retrieved from the PNDB; and finally, (3) molecular structures that match the possible partial structures are listed in order of number of hits. A molecular structure with a higher number of hits is more similar to the structure of the analyzed substance. The performance of the non-target method was evaluated by simulated analysis of 150 LC/HRMS spectra registered in MassBank. First, all substances of the same mass data (41/41) and 68% (39/57) of the mass data of the same substances not registered in the PNDB were elucidated. It was demonstrated that 14% (7/52) and 31% (16/52) of the substances with no mass spectral data registered in the PNDB were obtained at the first and within the fifth place, respectively. Owing to the fact that 10 of the total hits occurred in product ions and neutral losses, almost 50% of the substances evaluated with this method were placed at the top 4 positions in the similarity ranking. Importantly, the proposed method is effective for analyzing mass spectral data that has not been registered in the PNDB and thus is expected to be used for a variety of non-target analyses.

A feasible strategy to improve confident elemental composition determination of compounds in complex organic mixture such as natural organic matter by FTICR-MS without internal calibration

Confident elemental composition determination of compounds in complex samples such as natural organic matter (NOM) by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is challenging due to the interference between multiple components in these samples during detection. Here the performance of Solarix 15T-FTICR-MS in terms of accurate relative natural isotope abundance (RIA) and mass measurements for elemental composition determination of compounds in complex samples such as NOM was systematically evaluated. The optimal sweep excitation power values ranging from 20% to 22% was found to significantly diminish the underestimation of RIA measurement for ¹³C₁ peaks of NOM components by FTICR-MS. Random error was found to be one of the main sources for the RIA errors of ¹³C₁ peaks with S/N ratios <25. The mean averaged RIA errors of less than 10% could be obtained by averaging the measured RIAs of each ¹³C₁ peaks in five replicated runs. By adjusting the total ion abundance of NOM complex sample between 3.8-E7 and 1.4-E8 which was simultaneously similar to that of external calibrant during detection, mass errors of lower than 1 ppm for NOM components with m/z lower than 700 Da could be obtained without internal calibration. Meanwhile, a linear correlation between mass errors of ions in NOM complex sample and their m/z values could be obtained. The mass error deviation derived from the linearity was firstly used as new criterion to reduce the number of false formula candidates. A novel strategy of combination of high mass accuracy, high spectral accuracy, and mass error deviation for elemental composition determination of unknown compounds in complex sample such as NOM by FTICR-MS was proposed and applied for different complex samples. Compared to the traditional method, about one fold increasement in the number of the unique formula assignments for measured ions was obtained by using our strategy.

A simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines based on accurate mass, A + 1 and A + 2 isotopic peaks using Fourier transform ion cyclotron resonance mass spectrometry

RATIONALE

Recently, isotopic fine structures derived from Fourier transform ion cyclotron resonance mass spectrometry have been used to determine the molecular formula for unknown compounds in many complex systems. However, a simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines (TCMs) based on accurate mass, A + 1 and A + 2 isotopic peaks is necessary.

METHODS

Salviae miltiorrhizae was selected as a representative species. First, the chemical constituents were chromatographically separated and their accurate masses were obtained. The A + 1 and A + 2 isotopic peaks of all chemical constituents were then also acquired. Finally, the chemical formulae of the chemical constituents were determined.

RESULTS

In the sample of Salviae miltiorrhizae, the formulae of 38 CHO-containing chemical constituents were quickly determined, and all chemical constituents were identified using their tandem mass spectrometric data. Moreover, the method was validated by comparison of the A + 1 and A + 2 isotopic peaks, their fragmentation patterns and the retention times of six selected standard substances.

CONCLUSIONS

The results demonstrate that the described strategy performs well for molecular formula determination of chemical constituents in TCMs. This also indicates that this method will be meaningful for the structural identification of chemical constituents of TCMs.

Impact of method parameters on the performance of suspect screening for the identification of trace organic contaminants in surface waters

The performance of a suspect screening method to detect diverse small-molecule trace organic contaminants (TOCs) was systematically evaluated using a set of 39 model compounds. Experiments showed that ionization efficiency, ion transfer parameters, and chromatography could affect the detection of TOCs. As expected, compounds with low ionization yields and poorly retained compounds in chromatographic columns are more difficult to identify in the samples at environmental concentrations. Similarly, TOCs with large deviations from the average mass of the compounds screened were not transmitted efficiently in the mass spectrometer thus negatively affecting their detection. The suspect screening method was validated in terms of recovery and limits of identification of the model compounds using three different types of solid-phase extraction cartridges (reversed phase with polar groups, mixed-mode anion exchange, and mixed mode cation exchange). Experiments showed that more than two-thirds of the model compounds had recoveries >75% with each of the three cartridges, and comparison of limits of identification showed that more than one-half of the model compounds could be identified at concentrations between 6 and 100 ng L−1. However, it was observed that the amount of co-extracted compounds was higher in mixed-mode ion exchangers compared with the reversed-phase cartridge. Application of the suspect screening method using the three different cartridges to surface water samples showed that between 0 to 3% of the positive matches found by the peak identification algorithm were classified as probable structures. Solutions to improve suspect screening of TOCs are proposed and discussed.

In Situ Analysis of Surface Catalytic Reactions Using Shell-Isolated Nanoparticle-Enhanced Raman Spectroscopy

Electrochemistry and heterogeneous catalysis continue to attract enormous interest. In situ surface analysis is a dynamic research field capable of elucidating the catalytic mechanisms of reaction processes. Shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) is a nondestructive technique that has been cumulatively used to probe and analyze catalytic-reaction processes, providing important spectral evidence about reaction intermediates produced on catalyst surfaces. In this perspective, we review recent electrochemical- and heterogeneous-catalysis studies using SHINERS, highlight its advantages, summarize the flaws and prospects for improving the SHINERS technique, and give insight into its future research directions.

Restricted spectral accuracy analysis to identify the single correct organic compound elemental-composition from Orbitrap accurate mass data lists obtained at very high resolution

Restricted spectral accuracy is applied to Orbitrap data (240 000 resolution at m/z 400) to more clearly break out the scoring and ranking of allowable elemental compositions (ECs) in a candidate list. The correct EC is usually top ranked and separated from other answers by 10 to 40% within the dimensionless 0 to 100% scale, providing a single, definitive EC. The A + 2 position (where A denotes the monoisotopic line position) is especially advantageous in restricted spectral accuracy. It has enough intensity and more complexity than (A + 1) fine lines and is like a fingerprint. Avoidance of coalescence phenomena and careful ion population control are essential.

Method for the Routine Determination of Accurate Masses by Triple Quadrupole Mass Spectrometry

A new method for the measurement of accurate masses using direct infusion in an electrospray-triple quadrupole mass spectrometer is presented and compared to the traditional method using high-resolution mass spectrometry. The proposed method uses internal calibrants and post-acquisition calibration of the mass spectrum signal using the MassWorks software to determine accurate masses. Then, based on parameters such as elemental composition, number of double bond equivalents, and type of ion (even- or odd-electron), etc., a list of potential molecular formula candidates are generated and ranked according to spectral accuracy, (i.e., similarity between the calibrated profile and theoretical isotopic patterns). Experiments using six diverse synthesis products showed that mass accuracy in the Quattro Premier triple quadrupole mass spectrometer (QqQMS) was ≤9.2 mDa and spectral accuracy was ≥90.6%. According to both mass accuracy tolerance (±10 mDa) and spectral accuracy, the correct molecular formula was ranked in the top seven compounds out of up to 32 potential candidates. When considering the context of the synthesis reaction, only one formula was possible. In summary, results showed that the measurement of spectral accuracy in a low-resolution instrument such as the triple quadrupole was strongly dependent on the signal intensity and the presence of interfering peaks in the profile mass range window. This study suggests that use of triple quadrupole mass spectrometry followed by post-acquisition calibration can be an economical and robust approach compared to the traditional method using high-resolution mass spectrometers for the measurement of accurate masses in routine applications using small organic molecules at microgram-per-litter concentrations in relatively clean matrices.