Data analysis is a very challenging task in LC-MS metabolomic studies. The use of powerful analytical techniques (e.g., high-resolution mass spectrometry) provides high-dimensional data, often with noisy and collinear structures. Such amount of information-rich mass spectrometry data requires extensive processing in order to handle metabolomic data sets appropriately and to further assess sample classification/discrimination and biomarker discovery. This review shows the steps involved in the data analysis workflow for both targeted and untargeted metabolomic studies. Especial attention is focused on the distinct methodologies that have been developed in the last decade for the untargeted case. Furthermore, some powerful and recent alternatives based on the use of chemometric tools will also be discussed. In general terms, this review helps researchers to critically explore the distinct alternatives for LC-MS metabolomic data analysis to better choose the most appropriate for their case study.

Data analysis strategies for targeted and untargeted LC-MS metabolomic studies: Overview and workflow

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.

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

Clinical and forensic toxicology and doping control deal with hundreds or thousands of drugs that may cause poisoning or are abused, are illicit, or are prohibited in sports. Rapid and reliable screening for all these compounds of different chemical and pharmaceutical nature, preferably in a single analytical method, is a substantial effort for analytical toxicologists. Combined chromatography-mass spectrometry techniques with standardised reference libraries have been most commonly used for the purpose. In the last ten years, the focus has shifted from gas chromatography-mass spectrometry to liquid chromatography-mass spectrometry, because of progress in instrument technology and partly because of the polarity and low volatility of many new relevant substances. High-resolution mass spectrometry (HRMS), which enables accurate mass measurement at high resolving power, has recently evolved to the stage that is rapidly causing a shift from unit-resolution, quadrupole-dominated instrumentation. The main HRMS techniques today are time-of-flight mass spectrometry and Orbitrap Fourier-transform mass spectrometry. Both techniques enable a range of different drug-screening strategies that essentially rely on measuring a compound's or a fragment's mass with sufficiently high accuracy that its elemental composition can be determined directly. Accurate mass and isotopic pattern acts as a filter for confirming the identity of a compound or even identification of an unknown. High mass resolution is essential for improving confidence in accurate mass results in the analysis of complex biological samples. This review discusses recent applications of HRMS in analytical toxicology.

Current use of high-resolution mass spectrometry in drug screening relevant to clinical and forensic toxicology and doping control

Mass spectrometry is commonly applied to qualitatively and quantitatively profile small molecules, such as peptides, metabolites, or lipids. Modern mass spectrometers provide accurate measurements of mass-to-charge ratios of ions, with errors as low as 1 ppm. Even such high mass accuracy, however, is not sufficient to determine the unique chemical formula of each ion, and additional algorithms are necessary. Here we present a universal software tool for predicting chemical formulas from high-resolution mass spectrometry data, developed within the MZmine 2 framework. The tool is based on the use of a combination of heuristic techniques, including MS/MS fragmentation analysis and isotope pattern matching. The performance of the tool was evaluated using a real metabolomic data set obtained with the Orbitrap MS detector. The true formula was correctly determined as the highest-ranking candidate for 79% of the tested compounds. The novel isotope pattern-scoring algorithm outperformed a previously published met...

Highly accurate chemical formula prediction tool utilizing high-resolution mass spectra, MS/MS fragmentation, heuristic rules, and isotope pattern matching.

The most useful strategies for the alkylation of allylic systems are related to the Tsuji–Trost reaction or the use of different Lewis acids. Herein we report a photocatalytic approach for the allylation reaction of a variety of nucleophiles, such as heteroarenes, amines and alcohols. This method is compatible with a large variety of pyrroles and indoles, containing different substituents such as electron-withdrawing and electron-donating groups, unprotected nitrogen atoms and bromo derivatives. Moreover, this methodology enables the chromoselective synthesis of Z- or E-allylated compounds. While the use of UV-light irradiation has allowed the synthesis of the previously inaccessible Z-allylated products, E-isomers are prepared simply by changing both the light source to the visible region, and the catalytic system. Based on mechanistic and photochemical proofs, laser flash photolysis studies and DFT calculations, a rational mechanism is presented. Tsuji–Trost allylation is a traditional method for selective C-C bond formation that involves the use of palladium-based catalysts. Here, the authors report a metal-free, photocatalytic allylation of several heterocycles, amines and alcohols, which can be easily tuned towards the Z- or E- allylated product.

/pdf/chromoselective-access-to-z-or-e-allylated-amines-and-2upp5ymgf5.pdf

Chromoselective access to Z- or E- allylated amines and heterocycles by a photocatalytic allylation reaction.

Though MS has always appeared to be quite different from spectroscopy to analytical chemists who are familiar with both, a careful examination from historical and theoretical perspectives reveals a striking similarity between the two. With the introduction of spectral accuracy, a companion concept to the better known mass accuracy, new capabilities previously thought unfeasible can now be enabled for MS. (To listen to a podcast about this article, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html .).

https://pubs.acs.org/doi/pdfplus/10.1021/ac100888b

The Concept of Spectral Accuracy for MS

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The Concept of Spectral Accuracy for MS