Wiley Registry Research Articles

Plasma metabolite profiling and chemometric analyses of lung cancer along with three controls through gas chromatography-mass spectrometry.

Lung cancer has been the most common death causing cancer in the world for several decades. This study is focused on the metabolite profiling of plasma from lung cancer (LC) patients with three control groups including healthy non-smoker (NS), smokers (S) and chronic obstructive pulmonary disease patients (COPD) samples using gas chromatography-mass spectrometry (GC-MS) in order to identify the comparative and distinguishing metabolite pattern for lung cancer. Metabolites obtained were identified through National Institute of Standards and Technology (NIST) mass spectral (Wiley registry) and Fiehn Retention Time Lock (RTL) libraries. Mass Profiler Professional (MPP) Software was used for the alignment and for all the statistical analysis. 32 out of 1,877 aligned metabolites were significantly distinguished among three controls and lung cancer using p-value ≤ 0.001. Partial Least Square Discriminant Analysis (PLSDA) model was generated using statistically significant metabolites which on external validation provide high sensitivity (100%) and specificity (78.6%). Elevated level of fatty acids, glucose and acids were observed in lung cancer in comparison with control groups apparently due to enhanced glycolysis, gluconeogenesis, lipogenesis and acidosis, indicating the metabolic signature for lung cancer.

Metabolite profiling of human plasma by different extraction methods through gas chromatography–mass spectrometry—An objective comparison

For the comprehensive metabolite profiling of human plasma, sample preparation is a crucial step. In this investigation, we have compared 10 different extraction techniques for metabolite profiling by GC–MS. Six one-dimensional (1D) and four two-dimensional (2D) extraction techniques involving solvent precipitation, molecular weight cut off tube (MWCOT) and solid phase extraction (SPE) by using silica, RP C18, cation and anion were investigated. Pooled samples of 50 Healthy Male Plasma (HMP), 50 Healthy Female Plasma (HFP) and 100 Healthy Pakistani Plasma (HPP) were subjected to these extraction methods for comparison purposes. Metabolites obtained were identified through NIST mass spectral (Wiley registry), METLIN and Fiehn RTL libraries. XCMS Software was used for the detection of metabolic features, retention time correction, alignment, annotation and statistical analysis in each method. 116–34 peaks were detected by various methods and approx 33% of the peaks were characterized in each method. Hierarchical clustering of the 10 extraction methods showed a low similarity index (50.1%) which indicated different chemical nature of metabolites, resulting from different methods. Venn diagram highlights the GC–MS peaks (33–77%) common in various methods. Metabolites which were different in male and female groups were detected using a threshold value of p≤0.0001, q≤0.001 and fold change ≥3 by employing Welch's t-test and identified through METLIN. Results indicated that 2D-C18 and 2D-silica offers a comprehensive metabolite profile in term of reproducibility, number of peaks and difference in metabolite pattern of male and female.

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012.

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification.

Testing an alternative search algorithm for compound identification with the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’

A tandem mass spectral database system consists of a library of reference spectra and a search program. State-of-the-art search programs show a high tolerance for variability in compound-specific fragmentation patterns produced by collision-induced decomposition and enable sensitive and specific 'identity search'. In this communication, performance characteristics of two search algorithms combined with the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30,000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their setup from tandem-in-space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS.

Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data, MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library’

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the 'NIST/NIH/EPA Mass Spectral Library' (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross-validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library.

Detection and identification of drugs and toxicants in human body fluids by liquid chromatography–tandem mass spectrometry under data-dependent acquisition control and automated database search

Systematic toxicological analysis (STA) is aimed at detecting and identifying all substances of toxicological relevance (i.e. drugs, drugs of abuse, poisons and/or their metabolites) in biological material. Particularly, gas chromatography–mass spectrometry (GC/MS) represents a competent and commonly applied screening and confirmation tool. Herein, we present an untargeted liquid chromatography–tandem mass spectrometry (LC/MS/MS) assay aimed to complement existing GC/MS screening for the detection and identification of drugs in blood, plasma and urine samples. Solid-phase extraction was accomplished on mixed-mode cartridges. LC was based on gradient elution in a miniaturized C18 column. High resolution electrospray ionization-MS/MS in positive ion mode with data-dependent acquisition control was used to generate tandem mass spectral information that enabled compound identification via automated library search in the “Wiley Registry of Tandem Mass Spectral Data, MSforID”. Fitness of the developed LC/MS/MS method for application in STA in terms of selectivity, detection capability and reliability of identification (sensitivity/specificity) was demonstrated with blank samples, certified reference materials, proficiency test samples, and authentic casework samples.

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.

AROMA VOLATILE DIFFERENCES IN COMMERCIAL ORANGE-FLESHED CANTALOUPES, THE INBRED PARENTAL LINES AND STORED FRESH-CUTS

ISHS XXVI International Horticultural Congress: Issues and Advances in Postharvest Horticulture AROMA VOLATILE DIFFERENCES IN COMMERCIAL ORANGE-FLESHED CANTALOUPES, THE INBRED PARENTAL LINES AND STORED FRESH-CUTS

Comparative evaluations of mass spectral databases

This Communication presents a statistical analysis of the distributions of the National Institute of Standards and Technology/Environmental Protection Agency/Mass Spectrometry Data Center Mass Spectral Database and the Wiley Registry of Mass Spectra according to sizes (peaks per spectrum) of spectra. The differences in the distributions are explained in terms of the different philosophies under which the two databases were built. The Wiley Registry is a collection that attempts to include all available spectra, including spectra of unique compounds derived from the literature. The NIST collection selects primarily spectra of interest for chemical analysis.