A general procedure for finding potentially erroneous entries in the database of retention indices.

BACKGROUND: The NIST retention index database is one the most widely used sources of retention indices. In both untargeted analysis and machine learning studies filtering for potential errors is rather lacking or nonexistent. According to our estimates about 80% of the compounds from both NIST 17 and NIST 20 retention index databases have only one RI value per stationary phase, which makes searching for erroneous values with statistical methods impossible. Manual inspection is also impractical because the database contains more than 300 000 entries. RESULTS: We suggest a two-step procedure to find potentially erroneous retention indices based on machine learning. The first step is to use five predictive models to obtain predicted retention index values for the whole database. The second one is to compare these predicted values against the experimental ones. We consider a retention index erroneous if its accuracy (the difference between predicted and experimental value) is in the bottom 5% for each of the five models simultaneously. Using this method, we were able to detect 2093 outlier entries for standard and semi-standard non-polar stationary phases in the NIST 17 retention index database, 566 of those were corrected or removed by the developers in the NIST 20. SIGNIFICANCE: This is a novel approach to find potentially erroneous entries in a large-scale database with mostly unique entries, which can be applied not only to retention indices. The procedure can help filter and report mishandled data to improve the quality of the dataset for machine learning applications and experimental use.

Quantitative structure-property relationship modelling for predicting retention indices of essential oils based on an improved horse herd optimization algorithm.

The horse herd optimization algorithm (HOA), one of the more contemporary metaheuristic algorithms, has demonstrated superior performance in a number of challenging optimization tasks. In the present work, the descriptor selection issue is resolved by classifying different essential oil retention indices using the binary form, BHOA. Based on internal and external prediction criteria, Z-shape transfer functions (ZTF) were tested to verify their efficiency in improving BHOA performance in QSPR modelling for predicting retention indices of essential oils. The evaluation criteria involved the mean-squared error of the training and testing datasets (MSE), and leave-one-out internal and external validation (Q2). The degree of convergence of the proposed Z-shaped transfer functions was compared. In addition, K-fold cross validation with k = 5 was applied. The results show that ZTF, especially ZTF1, greatly improves the performance of the original BHOA. Comparatively speaking, ZTF, especially ZTF1, exhibits the fastest convergence behaviour of the binary algorithms. It chooses the fewest descriptors and requires the fewest iterations to achieve excellent prediction performance.

Use and abuse of retention indices in gas chromatography.

The value of the concept of retention indices (RI) to the practice of gas chromatography (GC) is highlighted, where the RI of a compound is one component of the strategy to identify the compound. The widespread reliance on GC and then on mass spectrometry for 'identification', may result in inadequate confirmation of molecular identity. However, RI do provide a useful tentative indication of the possible molecule(s). Thus, the RI value is a useful first measure of the molecule identity, and shown here to be valuable provided limitations are recognised. An author has a responsibility to correctly calculate the index and then use the values for (tentative) identification. Tables of reference RI values are useful in this respect, but finding an 'exact match' RI value does not confirm the identity. Hence, it is necessary to understand how the RI value may be incorrectly used in this respect. The reviewer of written research is charged with ensuring the index values are applied in a rigorous manner. Selected case studies from our own work, support the care that must be exercised when reporting RI values. In terms of advanced GC operations, mention is made of multidimensional gas chromatography and comprehensive two-dimensional gas chromatography to acquire RI values on both the first and second columns in the two-column separation experiment.

On the challenge of unambiguous identification of fentanyl analogs: Exploring measurement diversity using standard reference mass spectral libraries.

Fentanyl analogs are a class of designer drugs that are particularly challenging to unambiguously identify due to the mass spectral and retention time similarities of unique compounds. In this paper, we use agglomerative hierarchical clustering to explore the measurement diversity of fentanyl analogs and better understand the challenge of unambiguous identifications using analytical techniques traditionally available to drug chemists. We consider four measurements in particular: gas chromatography retention indices, electron ionization mass spectra, electrospray ionization tandem mass spectra, and direct analysis in real time mass spectra. Our analysis demonstrates how simultaneously considering data from multiple measurement techniques increases the observable measurement diversity of fentanyl analogs, which can reduce identification ambiguity. This paper further supports the use of multiple analytical techniques to identify fentanyl analogs (among other substances), as is recommended by the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG).

Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data.

Non-target analysis combined with liquid chromatography high resolution mass spectrometry is considered one of the most comprehensive strategies for the detection and identification of known and unknown chemicals in complex samples. However, many compounds remain unidentified due to data complexity and limited number structures in chemical databases. In this work, we have developed and validated a novel machine learning algorithm to predict the retention index (r[Formula: see text]) values for structurally (un)known chemicals based on their measured fragmentation pattern. The developed model, for the first time, enabled the predication of r[Formula: see text] values without the need for the exact structure of the chemicals, with an [Formula: see text] of 0.91 and 0.77 and root mean squared error (RMSE) of 47 and 67 r[Formula: see text] units for the NORMAN ([Formula: see text]) and amide ([Formula: see text]) test sets, respectively. This fragment based model showed comparable accuracy in r[Formula: see text] prediction compared to conventional descriptor-based models that rely on known chemical structure, which obtained an [Formula: see text] of 0.85 with an RMSE of 67.

Evidence for the Hydration of Some Organic Compounds during Reverse-Phase HPLC Analysis.

Some polar analytes (X) can reversibly form hydrates in water-containing eluents under the conditions of reversed-phase HPLC analysis, X + H2O ⇄ X × H2O. One of the methods to detect their formation is the recurrent approximation of the net retention times of such analytes, tR(C + ΔC) = atR(C) + b, where ΔC = const is the constant step in the variation of the organic modifier content of an eluent. These dependencies are linear if hydrates are not formed, but in the case of hydrate formation, they deviate from linearity under high water content. It has been shown that UV spectroscopic parameters, namely, relative optical densities: Arel = A(λ1)/A(λ2), depend on eluent composition for some organic compounds, but their variations cannot be used as indicators for hydrate formation. The coefficients that characterize the dependence of the analyte retention indices on the organic component concentration of an eluent, dRI/dC, appeared to be the most informative additional criterion for hydration. The values of these coefficients for most polar analytes are largely negative (dRI/dC < 0), whereas, for nonpolar compounds, they are largely positive (dRI/dC > 0).

Elucidation of the Lipid Composition of Hemp (Cannabis sativa L.) Products by Means of Gas Chromatography and Ultra-High Performance Liquid Chromatography Coupled to Mass Spectrometry Detection.

The growing demand in natural matrices that represent a source of dietary and nutraceutical molecules has led to an increasing interest in Cannabis sativa, considered to be a multipurpose, sustainable crop. Particularly, the considerable content in essential fatty acids (FAs) makes its derived-products useful food ingredients in the formulation of dietary supplements. In this research, the FA and triacylglycerol (TAG) composition of hempseed oils and flours were investigated using gas chromatography coupled to mass spectrometry and flame ionization detection as well as liquid chromatography coupled to mass spectrometry (LC-MS), respectively. Furthermore, a recently introduced linear retention index (LRI) approach in LC was successfully employed as a useful tool for the reliable identification of TAG species. A total of 30 FAs and 62 glycerolipids were positively identified in the investigated samples. Relative quantitative analyses confirmed linoleic acid as the most abundant component (50-55%). A favorable omega6/omega3 ratio was also measured in hemp-derived products, with the α-linolenic acid around 12-14%. Whereas, γ-linolenic acid was found to be higher than 1.70%. These results confirm the great value of Cannabis sativa as a source of valuable lipids, and the further improvement of the LRI system paves the way for the automatization of the identification process in LC.

Multi-objective evaluation of freshly distilled brandy: Characterisation and distribution patterns of key odour-active compounds.

The characterisation and distribution patterns of key odour-active compounds in head, heart1, heart2, tail, and stillage cuts of freshly distilled brandy were investigated by gas chromatography-olfactometry-mass spectrometry coupled with aroma extract dilution analysis (AEDA) and chemometrics analysis. Results from AEDA showed that there were 50, 61, 48, 25, and 18 odour-active compounds in the head, heart1, heart2, tail, and stillage cuts, respectively. Besides, 19, 22, 11, 5, and 4 quantified compounds with odour activity values ≥ 1, respectively, were considered to be potential contributors to the aroma profile of different distillation cuts. Especially, the chemometrics analysis illustrated the heart1 fraction was characterized by 3-methylbutanol, ethyl hexanoate, 1-hexanol, ethyl octanoate, benzaldehyde, ethyl decanoate, and 2-phenylethyl acetate; (E)-hex-3-en-1-ol, (Z)-hex-3-en-1-ol, and 2-phenylethyl acetate greatly contributed to the characteristics of the heart2 cut. Furthermore, different volatile compounds with a variety of boiling points and solubilities followed diverse distillation rules during the second distillation. Our findings may provide a rational basis for concentrating more pleasant aroma components contributing to brandy.

Dietary Intake of Coumarins and Furocoumarins through Citrus Beverages: A Detailed Estimation by a HPLC-MS/MS Method Combined with the Linear Retention Index System.

Official regulations concerning the maximum number of substances in food are introduced as a consequence of possible adverse effects, after oral administration. In this regard, analytical methods are necessary in order to determine specific targets. Among oxygen heterocyclic compounds (OHCs, that are furocoumarins, coumarins and polymethoxyflavones), only coumarin is subject to restriction by the Regulation (EC) No 1334/2008 of the European Parliament. Furocoumarins are known for their phototoxicity and other side effects due to their dietary intake; however, an official limit about the maximum content of these compounds in food is still missing. The lack of information about the real amount of these compounds in food is responsible for the conflicting opinions about the introduction of an official limit. The HPLC-MS/MS method here proposed, in combination with the linear retention index system, represents an innovative analytical strategy for the characterization of OHCs in citrus beverages. Several types of drinks were analysed in order to quantify 35 OHCs in total. This method is suitable for the quality control of OHCs in food and the obtained results may be considered as informative data useful for the regulatory authorities in the emission of new opinions and for a potential new regulation in this field.

Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics.

High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.

Chemical Characterization of Marrubium vulgare Volatiles from Serbia.

Marrubium vulgare is a cosmopolitan medicinal plant from the Lamiaceae family, which produces structurally highly diverse groups of secondary metabolites. A total of 160 compounds were determined in the volatiles from Serbia during two investigated years (2019 and 2020). The main components were E-caryophyllene, followed by germacrene D, α-humulene and α-copaene. All these compounds are from sesquiterpene hydrocarbons class which was dominant in both investigated years. This variation in volatiles composition could be a consequence of weather conditions, as in the case of other aromatic plants. According to the unrooted cluster tree with 37 samples of Marrubium sp. volatiles from literature and average values from this study, it could be said that there are several chemotypes: E-caryophyllene, ß-bisabolene, α-pinene, ß-farnesene, E-caryophyllene + caryophyllene oxide chemotype, and diverse (unclassified) chemotypes. However, occurring polymorphism could be consequence of adaptation to grow in different environment, especially ecological conditions such as humidity, temperature and altitude, as well as hybridization strongly affected the chemotypes. In addition, this paper aimed to obtain validated models for prediction of retention indices (RIs) of compounds isolated from M. vulgare volatiles. A total of 160 experimentally obtained RIs of volatile compounds was used to build the prediction models. The coefficients of determination were 0.956 and 0.964, demonstrating that these models could be used for predicting RIs, due to low prediction error and high r2.

Standardization of chromatographic signals - Part I: Towards obtaining instrument-agnostic fingerprints in gas chromatography.

One of the main causes for the sparse use of multivariate analytical methods in routine laboratory work is the dependency on the measuring instrument from which the analytical signal is acquired. This issue is especially critical in chromatographic equipment and results in limitations of their applicability. The solution to this problem is to obtain a standardized instrument-independent signal -or instrument-agnostic signal- regardless of the measuring instrument or of the state of the same instrument from which it has been acquired. The combined use of both internal and external standard series, allows us to have external and transferable references for the normalization of both the intensity and the position of each element of the data vector being arranged from the raw signal. From this information, a simple mathematical data treatment process is applied and instrument-agnostic signals can be secured. This paper describes and applies the proposed methodology to be followed for obtaining standardized instrumental fingerprints from two significant fractions of virgin olive oil (volatile organic compounds and triacylglycerols), obtained by gas chromatography coupled to mass spectrometry (GC-MS) and analysed with two temperature conditions (conventional and high-temperature, respectively). The results of both case studies show how the instrument-agnostic fingerprints obtained are coincidental, regardless of the state of the chromatographic system or the time of acquisition.

Thermodynamic modeling of comprehensive two dimensional gas chromatography isovolatility curves for second dimension retention indices based analyte identification.

A method to thermodynamically model the alkane isovolatility curves of a comprehensive two dimensional gas chromatography (GC × GC) separation is presented. This method omits all instrument modifications, additional chromatogram collection, or method alterations which typical isovolatility curve generation requires. Provided that the thermodynamic indices of reference alkanes are available, chromatographers only need to specify the GC × GC method parameters of their separation to output the isovolatility curves. The curves can then be used alongside reference retention indices to generate two dimensional retention times for each analyte. Agreement between the modeled and experimental retention times provides a secondary mechanism for compound identification, supporting the results of a mass spectral search. The technique was used to model the retention times of a GC × GC separation of aromatic hydrocarbons, achieving an average first dimension retention time modeling error of 11 s and an average second dimension retention time modeling error of 0.09 s. Retention indices modeled retention times provide a simpler analyte identification procedure compared to conventional two dimensional retention indices matching.

Gas chromatography/mass spectrometry analysis of reaction products of sulfur mustards with phenol.

Screening of chemicals related to chemical weapons convention including their all possible degradation and reaction products in environmental samples is important in the organization for prohibition of chemical weapons verification process. Sulfur mustards, commonly known as blistering agents, are included in schedule 1 chemicals of chemical weapons convention. Because of the presence of chlorine atoms in sulfur mustards, they are highly reactive and prone to react with other organic molecules such as phenols to produce corresponding reaction products. Thus, it is important to screen for not only the sulfur mustards but also their reaction products for verification process. The sulfur mustards and their degradation products have been routinely analyzed by gas chromatography/mass spectrometry method, however, the methods are yet to establish for the reaction products. In this study, the reaction products of the sulfur mustards with phenol (compounds 1-7) were studied by gas chromatography/mass spectrometry under electron ionization and chemical ionization conditions. The EI spectra of 1-7 displayed molecular ion and characteristic fragments that provided structure information. Mostly the fragment ions were due to homolytic cleavages involving C-O, C-S, and C-C cleavages. The methane or isobutane CI spectra showed M+., [M + H]+, and [M - H]+ ions including reagent specific adduct ions. The CI spectra also showed other adduct ions formed by association of analyte molecule with its most abundant fragment ion. The gas chromatography/retention index values were also calculated, which support unambiguous identification of targeted molecules in suspected environmental samples. The method was demonstrated for detection of the targeted molecules spiked in soil samples.

Characterization of 9 gas chromatography columns by Kovats and Lee retention indices for dioxin analysis.

Polychlorinated dibenzo-p-dioxins and furans offer a complex separation challenge due to their chemical similarity and 5020 possible congeners, including the Br/Cl congeners. Not only are these compounds difficult to separate, but they are also difficult to identify. Expensive reference materials are needed for conventional "dioxin analysis", usually requiring 13C labeled and native compounds. A retention index database offers a potential solution to lower the difficulty and cost to identify dioxins. This study describes the use of Kovats and Lee retention indices for the identification of chlorinated dioxins and furans as well as their brominated and mixed chloro/bromo counterparts. Eight columns were characterized with all 136 tetra through octa substituted chlorinated dioxins and furans as well as 32 brominated and mixed chloro/bromo congeners. Columns were then compared to identify which stationary phases provided the best resolution for critical congeners, like the 2,3,7,8 substituted compounds. Column phase selectivity was also investigated to identify best commercially-available column pairings for confirmatory analyses and GC × GC separations. The Rtx-Dioxin2 and Rxi-17SilMS showed unique selectivity for dioxins and furans and could be used as confirmatory columns or as a powerful GC × GC column set.

Identification of alkylpyrazines by gas chromatography mass spectrometry (GC-MS).

Pyrazines are an important group of natural products widely used as food additives and fragrants. Gas chromatography-mass spectrometry (GCMS) is the most widely applied analytical technique for characterization of alkylpyrazines. However, mass spectra of many positional isomers of alkylpyrazines are very similar. Consequently, an unambiguous identification of each positional isomer by spectral interpretation or database search protocols is practically unfeasible. In fact, there are many misidentifications in literature. To identify alkylpyrazines, chemists often resort to gas chromatographic retention indices (RIs). Although there are many compilations of retention indices of alkylpyrazines, these databases are often incomplete and the values reported are sometimes inconsistent. Herein, we present retention indices of fifty-six alkylpyrazines recorded on DB-1, ZB-5MS, DB-624, and ZB-WAXplus stationary phases, and compare them with those available in the NIST-2017 MS-RI database. Furthermore, we demonstrate how RI values can be used, together with mass spectral interpretations, to identify certain alkylpyrazines unambiguously.

Chemical composition and biological activity of the essential oil from the root of Jatropha pelargoniifolia Courb. native to Saudi Arabia.

The chemical composition of the essential oil from Jatropha pelargoniifolia roots was determined via GC-FID. There were 80 compounds, representing 99.99% of the total oil constituents. Among these, 77.31% were sesquiterpenes, 14.62% were fatty acids, 7.21% were other components (i.e., phenolics, hydrocarbons, etc.), and 0.85% were monoterpenes. The major compounds in the oil were γ-eudesmol (35.31%), 5-guaien-11-ol (14.43%), epi-cedrol (8.19%), oleic acid (5.23%), bulnesol (4.45%), α-linoleic acid (4.20%), 3,4-dimethoxycinnamic acid (3.83%), palmitic acid (2.69%), isolongifolanone (2.68%), eicosane (1.41%), and cedrol (1.14%). Oxygenated sesquiterpenes were found to represent more than 50% percent of the total oil content. Moreover, the essential oil was evaluated for anti-inflammatory, antioxidant, antipyretic, and antinociceptive activities using in vivo and in vitro models. Additionally, the antioxidant potential of the oil was evaluated using various in vitro antioxidant tests, including DPPH•, ABTS•+ and FRAP. At a dose of 240 µl/kg, the oil showed anti-inflammatory (59.12%), antipyretic (37.00 ±â€¯0.11), and antinociceptive (47.58%) activities and showed significant (p < 0.001) effect as compared to a standard drug (phenylbutazone and indomethacin). These findings demonstrated that the essential oil of Jatropha pelargoniifolia root could be used as a natural source for their anti-inflammatory, antinociceptive, antipyretic, and antioxidant effects.

Alkyl-Dimethylpyrazines in Mandibular Gland Secretions of Four Odontomachus Ant Species (Formicidae: Ponerinae).

Ponerine ants are known to contain mixtures of pyrazines in their mandibular glands. We analyzed the mandibular gland contents of four ponerine species (Odontomachus chelifer, O. erythrocephalus, O. ruginodis, and O. bauri) by gas chromatography coupled with mass spectrometry, and found that each species contains specific mixtures of trisubstituted alkylpyrazines among other volatiles. Attempts to identify alkylpyrazines solely by mass spectral interpretation is unrealistic because spectra of positional isomers are indistinguishable. To avoid misidentifications, we synthesized a large number of reference compounds and compared their mass spectral and gas chromatographic properties with those present in the Odontomachus species under investigation. Most of the compounds identified were 2-alkyl-3,5-dimethylpyrazines. Interestingly, when the third substituent was an isopentyl group, the two methyl groups were found to be located at the 2 and 5 ring positions. Using our data, we recognized several misidentifications in previous publications.

A retention index system for comprehensive two-dimensional gas chromatography using polyethylene glycols.

The characterization and identification of compounds in complex real-world samples is quite difficult and new concepts and workflows are highly desirable. Retention indices (RIs) are widely used in gas chromatography (GC) to support the identification of unknown compounds. Several attempts have been made to introduce a similar concept for the second dimension in comprehensive two-dimensional (2D) GC (GC × GC) but, an easily applicable and robust system remains elusive. In the present study, a new RI system for GC × GC was developed. Polyethylene glycols (PEGs) were used in combination with a simple linear regression, with n-alkanes as reference points for virtually unretained compounds and PEG homologs as reference compounds for second-dimension RIs (PEG-2I). The n-alkanes were assigned a PEG-2I of zero and the distance between consecutive PEG homologs from PEG-2 (diethylene glycol) and higher were assigned a PEG-2I value of 10. We used ethylene glycol and PEG-2 through PEG-10 as reference compounds, thereby covering a PEG-2I range from 20.0 for ethylene glycol, over 50.0 for diethylene glycol (PEG-2) to 130.0 for decaethylene glycol (PEG-10); additional PEGs can be added to cover a wider polarity range. The PEG-2I system was initially evaluated using a 30 m × 0.25 mm non-polar (5% phenyl, 0.25 µm film thickness) first-dimension column and a 1.6 m × 0.18 mm polar (50% phenyl, 0.18 µm film thickness) second-dimension column. This system was validated for use with non-polar first-dimension columns and a semi-polar (50% phenyl) second-dimension column, and exhibited robustness to changes in the carrier gas flow velocity, oven temperature ramping rate, and secondary oven temperature offset. An average relative standard deviation of 2.7%, equal to a 95% confidence interval of 1.27 PEG-2I units, was obtained for the PEG-2I values of 72 environmental pollutants. Additionally, the system was found to be applicable over a wide range of boiling points (in the current case, from n-heptane to n-dotriacontane (C7-C32)) and can be used with various column dimensions. Changing the second-dimension column to either a narrower 0.1 mm column or a wider 0.25 mm column, yielded similar 95%-percentiles to that of the 0.18 mm column, differing by only 3.20 and 2.80 PEG-2I units, respectively. Moreover, methods for improving the system were suggested.

Gas chromatographic retention behavior of polycyclic aromatic hydrocarbons (PAHs) and alkyl-substituted PAHs on two stationary phases of different selectivity.

Retention indices (I) for 45 polycyclic aromatic hydrocarbons (PAHs) and 63 methyl-substituted PAHs were determined by gas chromatography - mass spectrometry (GC-MS) using two different stationary phases: a Rxi-PAH phase (a "higher phenyl-content stationary phase") and a 50% (mole fraction) liquid crystalline dimethylpolysiloxane phase. Retention data were obtained for parent PAHs from molecular mass (MM) 128 g/mol (naphthalene) to 328 g/mol (benzo[c]picene) and for 12 sets of methyl-PAHs (methylfluorenes, methylanthracenes, methylphenanthrenes, methylfluoranthenes, methylpyrenes, methylbenz[a]anthracenes, methylbenzo[c]phenanthrenes, methylchrysenes, methyltriphenylenes, methylbenzo[a]pyrenes, methylperylenes, and methylpicenes). Molecular shape descriptors such as length-to-breath ratio (L/B) and thickness (T) were determined for all the PAHs studied. Correlation between I and L/B ratio was evaluated for both stationary phases with a better correlation observed for the 50% liquid crystalline phase (correlation coefficients ranging from 0.22 to 1.00). Graphical Abstract GC separation of six methylchrysene isomers (m/z 242) on two different stationary phases: 50 % phenyl-like methylpolysiloxane phase and 50 % liquid crystalline phase. Retention indices (I) are plotted as a function of L/B for both phases. The data marker numbers identify each isomer based on methyl-substitution position.