Identification of chemical compounds

Congruence Concept for Comparison of Spectra

This paper introduces an alternative, easy-to-implement spectrum comparison concept. The evaluation procedure is illustrated by artificial and attenuated total reflection Fourier transform infrared (ATR FT-IR) spectra, which it can also be extended to other spectrometries (e.g., ultraviolet-visible or UV-Vis and Raman). The evaluation for the comparison of two spectra is divided into four phases: (i) spectrum pre-treatment (e.g., smoothing and background correction), (ii) standard normal variate (SNV) transformation, (iii) regression analysis of SNV spectra, and (iv) calculation of the quantification index (FG). The FG is derived from the formula of R². It characterizes and quantifies the identity and/or similarity of the compared spectra.

BMDMS-NP: A comprehensive ESI-MS/MS spectral library of natural compounds

The Bioinformatics & Molecular Design Research Center Mass Spectral Library - Natural Products (BMDMS-NP) is a library containing the mass spectra of natural compounds, especially plant specialized metabolites. At present, the library contains the electrospray ionization tandem mass spectrometry (ESI-MS/MS) spectra of 2739 plant metabolites that are commercially available. The contents of the library were made comprehensive by incorporating data generated under various experimental conditions for compounds with diverse molecular structures. The structural diversity of the BMDMS-NP data was evaluated using molecular fingerprints, and it was sufficiently exhaustive enough to represent the structures of the natural products commercially available. The MS/MS spectra of each metabolite were obtained with different types/brands of ion traps (tandem-in-time) or combinations of mass analyzers (tandem-in-space) at multiple collision energies. All spectra were measured repeatedly in each environment because variations can occur in spectra, even under the same conditions. Moreover, the probability, separability of searching, and transferability of this spectral library were evaluated against those of MS/MS libraries, namely: NIST17 and MoNA.

Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data

High-resolution (HR) MS instruments recording HR-full scan allow analysts to go further beyond pre-acquisition choices. Untargeted acquisition can reveal unexpected compounds or concentrations and can be performed for preliminary diagnosis attempt. Then, revealed compounds will have to be identified for interpretations. Whereas the need of reference standards is mandatory to confirm identification, the diverse information collected from HRMS allows identifying unknown compounds with relatively high degree of confidence without reference standards injected in the same analytical sequence. However, there is a necessity to evaluate the degree of confidence in putative identifications, possibly before further targeted analyses. This is why a confidence scale and a score in the identification of (non-peptidic) known-unknown, defined as compounds with entries in database, is proposed for (LC-) HRMS data. The scale is based on two representative documents edited by the European Commission (2007/657/EC) and the Metabolomics Standard Initiative (MSI), in an attempt to build a bridge between the communities of metabolomics and screening labs. With this confidence scale, an identification (ID) score is determined as [a number, a letter, and a number] (e.g., 2D3), from the following three criteria: I, a General Identification Category (1, confirmed, 2, putatively identified, 3, annotated compounds/classes, and 4, unknown); II, a Chromatography Class based on the relative retention time (from the narrowest tolerance, A, to no chromatographic references, D); and III, an Identification Point Level (1, very high, 2, high, and 3, normal level) based on the number of identification points collected. Three putative identification examples of known-unknown will be presented. Graphical Abstract ᅟ.

Raman spectroscopy compatible PDMS droplet microfluidic culture and analysis platform towards on-chip lipidomics

Lipids produced by microalgae are viewed as a potential renewable alternative to fossil fuels, however, significant improvements in productivity are required for microalgal biofuels to become economically feasible. Here we present a method that allows for the use of Raman spectroscopy with poly(dimethylsiloxane) (PDMS) droplet microfluidic devices, which not only overcomes the high Raman background of PDMS, but also achieves pairing of the high-throughput single-cell resolution advantages of droplet microfluidics with the direct, chemically specific, label-free, and non-destructive nature of Raman spectroscopy. The platform was successfully utilized for in situ characterization of microalgal lipid production over time within droplets, paving the way towards high-throughput microalgal lipidomics assays.

Review: mass spectrometry in Russia

The present review covers the main research in the area of mass spectrometry from the 1990s which was about the same time as the Russian Federation emerged from the collapse of the Soviet Union (USSR). It consists of two main parts-application of mass spectrometry to chemistry and related fields and creation and development of mass spectrometric technique. Both traditional and comparatively new mass spectrometric methods were used to solve various problems in organic chemistry (reactivity of gas-phase ions, structure elucidation and problems of identification, quantitative and trace analysis, differentiation of stereoisomers, derivatization approaches etc.), biochemistry (proteomics and peptidomics, lipidomics), medical chemistry (mainly the search of biomarkers, pharmacology, doping control), environmental, petrochemistry, polymer chemistry, inorganic and physical chemistry, determination of natural isotope ratio etc. Although a lot of talented mass spectrometrists left Russia and moved abroad after the collapse of the Soviet Union, the vitality of the mass spectral community proved to be rather high, which allowed the continuation of new developments in the field of mass spectrometric instrumentation. They are devoted to improvements in traditional magnetic sector mass spectrometers and the development of new ion source types, to analysis and modification of quadrupole, time-of-flight (ToF) and ion cyclotron resonance (ICR) analyzers. The most important achievements are due to the creation of multi-reflecting ToF mass analyzers. Special attention was paid to the construction of compact mass spectrometers, particularly for space exploration, of combined instruments, such as ion mobility spectrometer/mass spectrometer and accelerating mass spectrometers. The comparatively young Russian Mass Spectrometry Society is working hard to consolidate the mass spectrometrists from Russia and foreign countries, to train young professionals on new appliances and regularly holds conferences on mass spectrometry. For ten years, a special journal Mass-spektrometria has published papers on all disciplines of mass spectrometry.

On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library. 3. Focus on ion trap and upfront CID

Mass spectral libraries represent versatile tools for the identification of small bioorganic molecules. Libraries based on electron impact spectra are rated robust and transferable. Tandem mass spectral libraries are often considered to work properly only on the instrument that has been used to build the library. An exception from that rule is the 'Wiley Registry of Tandem Mass Spectral Data, MSforID'. In various studies with data sets from different kinds of tandem mass spectrometric instruments, the outstanding sensitivity and robustness of this tandem mass spectral library search approach was demonstrated. The instrumental platforms tested, however, mainly included various tandem-in-space instruments. Herein, the results of a multicenter study with a focus on upfront and tandem-in-time fragmentation are presented. Five laboratories participated and provided fragment ion mass spectra from the following types of mass spectrometers: time-of-flight (TOF), quadrupole-hexapole-TOF, linear ion trap (LIT), 3-D ion trap and LIT-Orbitrap. A total number of 1231 fragment ion mass spectra were collected from 20 test compounds (amiloride, buphenin, cinchocaine, cyclizine, desipramine, dihydroergotamine, dyxirazine, dosulepin, ergotamine, ethambutol, etofylline, mefruside, metoclopramide, phenazone, phentermine, phenytoin, sulfamethoxazole, sulfamoxole, sulthiame and tetracycline) on seven electrospray ionization instruments using 18 different instrumental configurations for fragmentation. For 1222 spectra (99.3%), the correct compound was retrieved as the best matching compound. Classified matches (matches with 'relative average match probability' >40.0) were obtained for 1207 spectra (98.1%). This high percentage of correct identifications clearly supports the hypothesis that the tandem mass spectral library approach tested is a robust and universal identification tool.

Separation and identification of flavonoids from complex samples using off-line two-dimensional liquid chromatography tandem mass spectrometry

In this study, a LC-based identification strategy was proposed and off-line two-dimensional liquid chromatography was developed for the separation and identification of flavonoids from complex samples. The highly orthogonal separation system was composed of a CD column, an OEG column and an XTerra C(18) column. The CD column was employed for the first dimensional separation and the OEG column and XTerra C(18) column were used for the second dimensional separation in parallel. A mixture of six traditional Chinese medicines was used as a complex sample in testing this method. Unknown peaks were identified by matching their retention times and accurate mass molecular weights with those of references. The identification efficacy of parallel unidimensional liquid chromatography and off-line two-dimensional liquid chromatography was compared, and the latter was demonstrated to be more efficient for the identification of target compounds-especially co-eluted compounds or minor compounds from complex samples.

Qualitative aspects in the analysis of pesticide residues in fruits and vegetables using fast, low-pressure gas chromatography-time-of-flight mass spectrometry

Quantitative method validation is a well-established process to demonstrate trueness and precision of the results with a given method. However, an assessment of qualitative results is also an important need to estimate selectivity and devise criteria for chemical identification when using the method, particularly for mass spectrometric analysis. For multianalyte analysis, automatic instrument software is commonly used to make initial qualitative identifications of the target analytes by comparison of their mass spectra against a database library. Especially at low residue levels in complex matrices, manual checking of results is typically needed to correct the peak assignments and integration errors, which is very time-consuming. Low-pressure gas chromatography-mass spectrometry (LP-GC-MS) has been demonstrated to increase the speed of analysis for GC-amenable residues in various foods and provide more advantages over the traditional GC-MS approach. LP-GC-MS on a time-of-flight (ToF) instrument was used, which provided high sample throughput with <10 min analysis time. The method had already been validated to be acceptable quantitatively for nearly 150 pesticides, and in this study of qualitative performance, 90 samples in total of strawberry, tomato, potato, orange, and lettuce extracts from the QuEChERS sample preparation approach were analyzed. The extracts were randomly spiked with different pesticides at different levels, both unknown to the analyst, in the different matrices. Automated software evaluation was compared with human assessments in terms of false-positive and -negative results. Among the 13590 possible permutations with 696 blind additions made, the automated software approach yielded 1.2% false presumptive positives with 23% false negatives, whereas the analyst achieved 0.8% false presumptive positives and 17% false negatives for the same analytical data files. False negatives frequently occurred due to challenges at the lowest concentrations, but 70% of them involved certain pesticides that degraded (e.g., captafol, folpet) or otherwise could not be detected. The false-negative rate was reduced to 5-10% if the problematic analytes were excluded. Despite its somewhat better performance in this study, the analyst approach was extremely time-consuming and would not be practical in high sample throughput applications for so many analytes in complicated matrices.

On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study

The inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library originally built on a quadrupole-quadrupole-time-of-flight instrument was examined. The library consisted of 3759 MS/MS spectra collected from 402 reference compounds applying several different collision-energy values for fragmentation. In the course of the multicenter study, 22 test compounds were sent to three different laboratories, where 418 tandem mass spectra were acquired using four different instruments from two manufacturers. The study covered the following types of tandem mass spectrometers: quadrupole-quadrupole-time-of-flight, quadrupole-quadrupole-linear ion trap, quadrupole-quadrupole-quadrupole, and linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer. In each participating laboratory, optimized instrumental parameters were gathered solely from routinely applied workflows. No standardization procedure was applied to increase the inter-instrument comparability of MS/MS spectra. The acquired tandem mass spectra were matched against the established reference library using a sophisticated matching algorithm, which is presented in detail in a companion paper. Correct answers, meaning that the correct compound was retrieved as top hit, were obtained in 98.1% of cases. For the remaining 1.9% of spectra, the correct compound was matched at second rank. The observed high percentage of correct assignments clearly suggests that the developed mass spectral library search approach is to a large extent platform independent.

Determination of ion structures in structurally related compounds using precursor ion fingerprinting

Structurally-related alkaloids were analyzed by electrospray ionization/multiple stage mass spectrometry (ESI/MS(n)) at varying collision energies to demonstrate a conceptual algorithm, precursor ion fingerprinting (PIF). PIF is a new approach for interpreting and library-searching ESI mass spectra predicated on the precursor ions of structurally-related compounds and their matching product ion spectra. Multiple-stage mass spectra were compiled and constructed into "spectral trees" that illustrated the compounds' product ion spectra in their respective mass spectral stages. The precursor ions of these alkaloids were characterized and their spectral trees incorporated into an MS(n) library. These data will be used to construct a universal, searchable, and transferable library of MS(n) spectra. In addition, PIF will generate a proposed structural arrangement utilizing previously characterized ion structures, which will assist in the identification of unknown compounds.

Pitfalls and Prevention Strategies for Liquid Chromatography-Tandem Mass Spectrometry in the Selected Reaction– Monitoring Mode for Drug Analysis

Background: We observed cases of false-positive results with the use of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Different LC-MS/MS techniques that use the selected reaction-monitoring mode, routinely employed for the analysis and quantification of drugs and toxic compounds in biological matrices, were involved in the false-positive and potentially false-positive results obtained. We sought to analyze the causes of and solutions to this problem.

Methods: We used a previously reported LC-MS/MS general unknown screening method, as well as manual spectral investigation in 1 case, to perform verification and identification of interfering compounds.

Results: We observed that false-positive results involved: a metabolite of zolpidem that might have been mistaken for lysergic acid diethylamide, benzoylecgonine mistaken for atropine, and clomipramine and 3 phenothiazines that share several common ion transitions.

Conclusions: To prevent problems such as those we experienced, we recommend the use of stable-isotope internal standards when possible, relative retention times, 2 transitions or more per compound when possible, and acceptable relative abundance ratios between transitions, with an experience-based tolerance of ±15% for transitions with a relative abundance &gt;10% and with an extension to ±25% for transitions &lt;10% when the concentration is at the limit of quantification. A powerful general unknown screening procedure can help to confirm suspected interferences. Our results indicate that the specificity of screening procedures is questionable for LC-MS/MS analyses performed in the selected reaction-monitoring mode and involving a large number of compounds with only 1 transition per compound.

Retention indices in the analysis of food aroma volatile compounds in temperature-programmed gas chromatography: Database creation and evaluation of precision and robustness

A retention index (RI) database containing 250 volatile compounds was created on a polar stationary phase column and validated for food aroma characterisation. Precision of the retention indices (RIs) was assessed by performing replicated injections of a representative number of volatiles under the same experimental conditions: differences lower than 1 U were observed for all the compounds. Robustness was evaluated by carrying out injections of the same set of volatile compounds under different experimental conditions, i.e. program temperature, column batches and instrumentation. Excellent results were obtained with a maximum difference in the RI values of 10 U. The capabilities of the created database for food aroma characterisation were finally evaluated by analysing the volatile fractions of different food matrices such as dry sausages, cheese and bread. A great number of volatile compounds were identified in the analysed samples on the basis of their RI, thus proving the usefulness of the RI collections in the field of food analysis.

Evaluation of the hypothesis that Balkan endemic nephropathy is caused by drinking water exposure to contaminants leaching from Pliocene coal deposits

Balkan endemic nephropathy (BEN) is a kidney disease that has been reported in only certain rural villages in Serbia, Bulgaria, Romania, Croatia and Bosnia. The cause of BEN remains a mystery, but researchers seem to agree that exposure to one or more environmental agents is at least partially responsible. The Pliocene lignite hypothesis suggests the disease is due to long-term exposure to polycyclic aromatic hydrocarbons (PAHs) or other toxic organic compounds that have leached into drinking water supplies from low-rank coals. Although this hypothesis has been promoted by some researchers, efforts to substantiate it have been inconclusive due to limitations in sample size and methodology. The present study was designed to further examine this hypothesis by analyzing PAHs, which were implicated in the original hypothesis, in a larger number of water samples from endemic and nonendemic villages in Bulgaria and for other chemical differences between the villages. Results show that levels of all PAHs were low, with none exceeding the drinking water standard for benzo-[a]-pyrene, the most toxic PAH, and the only one for which a maximum contaminant level (MCL) has been set for drinking water. Comparison of additional unidentified chromatographic peaks from high-pressure liquid chromatography (HPLC) technique designed to detect dissolved organic compounds (DOCs) that leach from coal failed to show higher levels in BEN villages. This study finds no basis to connect PAHs or other unknown DOCs to the etiology of BEN, and suggests that the evidence in support of the Pliocene lignite hypothesis is limited to the spatial association originally proposed.

Time of flight mass spectrometry applied to the liquid chromatographic analysis of pesticides in water and food

Liquid chromatography coupled to mass spectrometry (LC-MS) is an excellent technique to determine trace levels of polar and thermolabile pesticides and their degradation products in complex matrices. LC-MS can be equipped with several mass analyzers, each of which provides unique features capable to identify, quantify, and resolve ambiguities by selecting appropriate ionization and acquisition parameters. We discuss in this review the use of LC coupled to (quadrupole) time-of-flight mass spectrometry (LC-(Q)ToF-MS) to determine the presence of target and non-target pesticides in water and food. This technique is characterized by operating at a resolving power of 10,000 or more. Therefore, it gives accurate masses for both parent and fragment ions and enables the measurement of the elemental formula of a compound achieving compound identification. In addition, the combination of quadrupole-ToF permits tandem mass spectrometry, provides more structural information, and enhances selectivity. The purpose of this article is to provide an overview on the state of art and applicability of liquid chromatography time-of-flight mass spectrometry (LC-ToF-MS), and liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS) for the analysis of pesticides in environmental matrices and food. The performance of such techniques is depicted in terms of accurate mass measurement, fragmentation, and selectivity. The final section is devoted to describing the applicability of LC-(Q)ToF-MS to routine analysis of pesticides in food matrices, indicating those operational conditions and criteria used to screen, quantify, and identify target and "suspected" pesticides and their degradation products in water, fruits, and vegetables. The potential and future trends as well as limitations of LC-(Q)ToF-MS for pesticide monitoring are highlighted.

Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs

The potential of the combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for the identification of therapeutic and illicit drugs has been evaluated. Reserpine was used for standardizing experimental conditions and for characterization of the performance of the applied mass spectrometric system. Experiments revealed that because of the mass accuracy, the stability of calibration, and the reproducibility of fragmentation, the QqTOF mass spectrometer is an appropriate platform for establishment of a tandem-mass-spectral library. Three-hundred and nineteen substances were used as reference samples to build the spectral library. For each reference compound, product-ion spectra were acquired at ten different collision-energy values between 5 eV and 50 eV. For identification of unknown compounds, a library search algorithm was developed. The closeness of matching between a measured product-ion spectrum and a spectrum stored in the library was characterized by a value called "match probability", which took into account the number of matched fragment ions, the number of fragment ions observed in the two spectra, and the sum of the intensity differences calculated for matching fragments. A large value for the match probability indicated a close match between the measured and the reference spectrum. A unique feature of the library search algorithm-an implemented spectral purification option-enables characterization of multi-contributor fragment-ion spectra. With the aid of this software feature, substances comprising only 1.0% of the total amount of binary mixtures were unequivocally assigned, in addition to the isobaric main contributors. The spectral library was successfully applied to the characterization of 39 forensic casework samples.

Towards a full reference library of MS(n) spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds

A library consisting of 3766 MS(n) spectra of 1743 compounds, including 3126 MS2 spectra acquired mainly using ion trap (IT) and triple-quadrupole (QqQ) instruments, was composed of numerous collections/sources. Ionization techniques were mainly electrospray ionization and also atmospheric pressure chemical ionization and chemical ionization. The library was tested for the performance in identification of unknowns, and in this context this work is believed to be the largest of all known tests of product-ion mass spectral libraries. The MS2 spectra of the same compounds from different collections were in turn divided into spectra of 'unknown' and reference compounds. For each particular compound, library searches were performed resulting in selection by taking into account the best matches for each spectral collection/source. Within each collection/source, replicate MS2 spectra differed in the collision energy used. Overall, there were up to 950 search results giving the best match factors and their ranks in corresponding hit lists. In general, the correct answers were obtained as the 1st rank in up to 60% of the search results when retrieved with (on average) 2.2 'unknown' and 6.2 reference replicates per compound. With two or more replicates of both 'unknown' and reference spectra (the average numbers of replicates were 4.0 and 7.8, respectively), the fraction of correct answers in the 1st rank increased to 77%. This value is close to the performance of established electron ionization mass spectra libraries (up to 79%) found by other workers. The hypothesis that MS2 spectra better match reference spectra acquired using the same type of tandem mass spectrometer (IT or QqQ) was neither strongly proved nor rejected here. The present work shows that MS2 spectral libraries containing sufficiently numerous different entries for each compound are sufficiently efficient for identification of unknowns and suitable for use with different tandem mass spectrometers.