Determination of the elemental composition of trace analytes in complex matrices using exact masses of product ions and corresponding neutral losses

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation

The identification of unknown molecules has been one of the cornerstone applications of mass spectrometry for decades. This tutorial reviews the basics of the interpretation of electrospray ionization-based MS and MS/MS spectra in order to identify small-molecule analytes (typically below 2000 Da). Most of what is discussed in this tutorial also applies to other atmospheric pressure ionization methods like atmospheric pressure chemical/photoionization. We focus primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds, rather than describing strategies for large-scale identification in complex samples. We critically discuss topics like the detection of protonated and deprotonated ions ([M + H]+ and [M - H]- ) as well as other adduct ions, the determination of the molecular formula, and provide some basic rules on the interpretation of product ion spectra. Our tutorial focuses primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds (eg, contaminants in chemical production, pharmacological alteration of drugs), rather than describing strategies for large-scale identification in complex samples. This tutorial also discusses strategies to obtain useful orthogonal information (UV/Vis, H/D exchange, chemical derivatization, etc) and offers an overview of the different informatics tools and approaches that can be used for structural elucidation of small molecules. It is primarily intended for beginning mass spectrometrists and researchers from other mass spectrometry sub-disciplines that want to get acquainted with structural elucidation are interested in some practical tips and tricks.

Product ion isotopologue pattern: A tool to improve the reliability of elemental composition elucidations of unknown compounds in complex matrices

RATIONALE

Elucidation of the elemental compositions of unknown compounds (e.g., in metabolomics) generally relies on the availability of accurate masses and isotopic ratios. This study focuses on the information provided by the abundance ratio within a product ion pair (monoisotopic versus the first isotopic peak) when isolating and fragmenting the first isotopic ion (first isotopic mass spectrum) of the precursor.

METHODS

This process relies on the capability of the quadrupole within the Q Orbitrap instrument to isolate a very narrow mass window. Selecting only the first isotopic peak (first isotopic mass spectrum) leads to the observation of a unique product ion pair. The lighter ion within such an isotopologue pair is monoisotopic, while the heavier ion contains a single carbon isotope. The observed abundance ratio is governed by the percentage of carbon atoms lost during the fragmentation and can be described by a hypergeometric distribution.

RESULTS

The observed carbon isotopologue abundance ratio (product ion isotopologue pattern) gives reliable information regarding the percentage of carbon atoms lost in the fragmentation process. It therefore facilitates the elucidation of the involved precursor and product ions. Unlike conventional isotopic abundances, the product ion isotopologue pattern is hardly affected by isobaric interferences. Furthermore, the appearance of these pairs greatly aids in cleaning up a 'matrix-contaminated' product ion spectrum.

CONCLUSIONS

The product ion isotopologue pattern is a valuable tool for structural elucidation. It increases confidence in results and permits structural elucidations for heavier ions. This tool is also very useful in elucidating the elemental composition of product ions. Such information is highly valued in the field of multi-residue analysis, where the accurate mass of product ions is required for the confirmation process. Copyright © 2016 John Wiley & Sons, Ltd.

Identification of metabolites and thermal transformation products of quinolones in raw cow's milk by liquid chromatography coupled to high-resolution mass spectrometry

The presence of residues of antibiotics, metabolites, and thermal transformation products (TPs), produced during thermal treatment to eliminate pathogenic microorganisms in milk, could represent a risk for people. Cow's milk samples spiked with enrofloxacin (ENR), ciprofloxacin (CIP), difloxacin (DIF), and sarafloxacin (SAR) and milk samples from cows medicated with ENR were submitted to several thermal treatments. The milk samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to find and identify TPs and metabolites. In this work, 27 TPs of 4 quinolones and 24 metabolites of ENR were found. Some of these compounds had been reported previously, but others were characterized for the first time, including lactose-conjugated CIP, the formamidation reaction for CIP and SAR, and hydroxylation or ketone formation to produce three different isomers for all quinolones studied.

Spectral accuracy of a new hybrid quadrupole time-of-flight mass spectrometer: application to ranking small molecule elemental compositions

RATIONALE

Determining the elemental compositions of unknown molecules is an important goal of analytical chemistry. The isotope pattern revealed by a mass spectrometer provides valuable information regarding the elemental composition of a molecule. In order to employ spectral accuracy considerations for elemental composition determination, it is important to know how faithfully a mass spectrometer can record the isotope pattern and to understand the magnitude of the errors of the relative isotopic abundances.

METHODS

Twenty-four small molecule drugs and two natural products representing a diverse range of elemental compositions and ranging in molecular weight from 236 to 1663 Da were measured on a new hybrid orthogonal acceleration quadrupole time-of-flight (Q-TOF) mass spectrometer by flow infusion analysis. The similarity between the observed profile isotope pattern and the theoretical isotope pattern, denoted spectral accuracy, was calculated using a computational algorithm in the program MassWorks.

RESULTS

The spectral accuracy for all compounds averaged better than 98%. When using spectral accuracy to rank elemental compositions with the elemental constraints (C(1-100)H(0-200)N(0-50)O(0-50)F(0-5)S(0-5)Cl(0-5)Br(0-5)) further restricted by empirical rules and a mass tolerance ≤5 parts-per-million, the correct formula was ranked first over 80% of the time. In contrast, when using mass accuracy for ranking, only two compounds (8%) were ranked first. For quinidine and troglitazone, the initial spectral accuracy measurements were lower than expected and further analysis indicated that minor, structurally related components were present.

CONCLUSIONS

Our work has determined the magnitude of spectral accuracy that can be expected on a new Q-TOF mass spectrometer. In addition, we demonstrate the utility of spectral accuracy measurements both for ranking elemental compositions and also for obtaining insight into the chemical nature of the analyte that might otherwise be overlooked.

Current mass spectrometry strategies for the analysis of pesticides and their metabolites in food and water matrices

Analysis of pesticides and their metabolites in food and water matrices continues to be an active research area closely related to food safety and environmental issues. This review discusses the most widely applied mass spectrometric (MS) approaches to pesticide residues analysis over the last few years. The main techniques for sample preparation remain solvent extraction and solid-phase extraction. The QuEChERS (Quick, Easy, Cheap, Effective, Rugged, Safe) approach is being increasingly used for the development of multi-class pesticide residues methods in various sample matrices. MS detectors-triple quadrupole (QqQ), ion-trap (IT), quadrupole linear ion trap (QqLIT), time-of-flight (TOF), and quadrupole time-of-flight (QqTOF)-have been established as powerful analytical tools sharing a primary role in the detection/quantification and/or identification/confirmation of pesticides and their metabolites. Recent developments in analytical instrumentation have enabled coupling of ultra-performance liquid chromatography (UPLC) and fast gas chromatography (GC) with MS detectors, and faster analysis for a greater number of pesticides. The newly developed "ambient-ionization" MS techniques (e.g., desorption electrospray ionization, DESI, and direct analysis in real time, DART) hyphenated with high-resolution MS platforms without liquid chromatography separation, and sometimes with minimum pre-treatment, have shown potential for pesticide residue screening. The recently introduced Orbitrap mass spectrometers can provide high resolving power and mass accuracy, to tackle complex analytical problems involved in pesticide residue analysis.

Identification of "known unknowns" utilizing accurate mass data and chemical abstracts service databases

In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others.

Strategy for the elucidation of elemental compositions of trace analytes based on a mass resolution of 100,000 full width at half maximum

Elemental compositions (ECs) can be elucidated by evaluating the high-resolution mass spectra of unknown or suspected unfragmented analyte ions. Classical approaches utilize the exact mass of the monoisotopic peak (M + 0) and the relative abundance of isotope peaks (M + 1 and M + 2). The availability of high-resolution instruments like the Orbitrap currently permits mass resolutions up to 100,000 full width at half maximum. This not only allows the determination of relative isotopic abundances (RIAs), but also the extraction of other diagnostic information from the spectra, such as fully resolved signals originating from (34)S isotopes and fully or partially resolved signals related to (15)N isotopes (isotopic fine structure). Fully and partially resolved peaks can be evaluated by visual inspection of the measured peak profiles. This approach is shown to be capable of correctly discarding many of the EC candidates which were proposed by commercial EC calculating algorithms. Using this intuitive strategy significantly extends the upper mass range for the successful elucidation of ECs.

Identification/quantification of multiple pesticide residues in food plants by ultra-high-performance liquid chromatography-time-of-flight mass spectrometry

In this study, the potential of ultra-high-performance liquid chromatography coupled with the time-of-flight mass spectrometry (UHPLC-TOF MS) to enable rapid and comprehensive analysis of 212 pesticide residues in QuEChERS extracts obtained from four plant matrices has been investigated. Method optimization is discussed in detail. In addition to molecular adducts, also fragment ions were provided for all target pesticides, thus obtaining at least three identification points required by European Decision 2002/657/EC was achieved. To get maximum information on analytes present in the extracts, each sample was examined within two injections, the first in a positive and the next one in a negative ionization mode. Under UHPLC conditions, both analyses were completed within 24min. For more than 96% of pesticides involved in this study, the limit of quantification was < or =10micro/kg. As a part of the work, strategy enabling screening of non-target pesticides and their metabolites is demonstrated on analysis of real-life samples.

Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches

BACKGROUND

In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed.

METHODOLOGY/PRINCIPAL FINDINGS

The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30-50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries.

CONCLUSIONS/SIGNIFICANCE

High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data.

Automated determination of precursor ion, product ion, and neutral loss compositions and deconvolution of composite mass spectra using ion correlation based on exact masses and relative isotopic abundances

After an accidental, deliberate, or weather-related dispersion of chemicals (dispersive event), rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A direct analysis in real time (DART)ion source interfaced to a JEOL AccuTOFmass spectrometer provided exact masses accurate to within 2 mDa for most ions in full scan mass spectra and relative isotopic abundances (RIAs) accurate to within 15-20% for abundant isotopic ions. To speed determination of the correct composition for precursor ions and most product ions and neutral losses, a three-part software suite was developed. Starting with text files of m/z ratios and their ion abundances from mass spectra acquired at low, moderate, and high collision energies, the ion extraction program (IEP) compiled lists for the most abundant monoisotopic ions of their exact masses and the RIAs of the +1 and +2 isotopic peaks when abundance thresholds were met; precursor ions; and higher-mass, precursor-related species. The ion correlation program (ICP) determined if a precursor ion composition could yield a product ion and corresponding neutral loss compositions for each product ion in turn. The input and output program (IOP) provided the ICP with each precursor ion:product ion pair for multiple sets of error limits and prepared correlation lists for single or multiple precursor ions. The software determined the correct precursor ion compositions for 21 individual standards and for three- and seven-component mixtures. Partial deconvolution of composite mass spectra was achieved based on exact masses and RIAs, rather than on chromatography.