Bootstrap classification and point-based feature selection from age-staged mouse cerebellum tissues of matrix assisted laser desorption/ionization mass spectra using a fuzzy rule-building expert system

A bootstrap method for point-based detection of candidate biomarker peaks has been developed from pattern classifiers. Point-based detection methods are advantageous in comparison to peak-based methods. Peak determination and selection are problematic when spectral peaks are not baseline resolved or on a varying baseline. The benefit of point-based detection is that peaks can be globally determined from the characteristic features of the entire data set (i.e., subsets of candidate points) as opposed to the traditional method of selecting peaks from individual spectra and then combining the peak list into a data set. The point-based method is demonstrated to be more effective and efficient using a synthetic data set when compared to using Mahalanobis distance for feature selection. In addition, probabilities that characterize the uniqueness of the peaks are determined.This method was applied for detecting peaks that characterize age-specific patterns of protein expression of developing and adult mouse cerebella from matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) data. The mice comprised three age groups: 42 adults, 19 14-day-old pups, and 16 7-day-old pups. Three sequential spectra were obtained from each tissue section to yield 126, 57 and 48 spectra for adult, 14-day-old pup, and 7-day-old pup spectra, respectively. Each spectrum comprised 71,879 mass measurements in a range of 3.5-50 kDa. A previous study revealed that 846 unique peaks were detected that were consistent for 50% of the mice in each age group (C. Laurent, D.F. Levinson, S.A. Schwartz, P.B. Harrington, S.P. Markey, R.M. Caprioli, P. Levitt, Direct profiling of the cerebellum by MALDI MS: a methodological study in postnatal and adult mouse, J. Neurosci. Res. 81 (2005) 613-621.).A fuzzy rule-building expert system (FuRES) was applied to investigate the correlation of age with features in the MS data. FuRES detected two outlier pup-14 spectra. Prediction was evaluated using 100 bootstrap samples of 2 Latin-partitions (i.e., 50:50 split between training and prediction set) of the mice. The spectra without the outliers yielded classification rates of 99.1 ± 0.1%, 90.1 ± 0.8%, and 97.0 ± 0.6% for adults, 14-day-old pups, and 7-day-old pups, respectively. At a 95% level of significance, 100 bootstrap samples disclosed 35 adult and 21 pup distinguishing peaks for separating adults from pups; and 8 14-day-old and 15 7-day-old predictive peaks for separating 14-day-old pup from 7-day-old pup spectra. A compressed matrix comprising 40,393 points that were outside the 95% confidence intervals of one of the two FuRES discriminants was evaluated and the classification improved significantly for all classes. When peaks that satisfied a quality criterion were integrated, the 55 integrated peak areas furnished significantly improved classification for all classes: the selected peak areas furnished classification rates of 100%, 97.3 ± 0.6%, and 97.4 ± 0.3% for adult, 14-day-old pups, and 7-day-old pups using 100 bootstrap Latin partitions evaluations with the predictions averaged. When the bootstrap size was increased to 1000 samples, the results were not significantly affected. The FuRES predictions were consistent with those obtained by discriminant partial least squares (DPLS) classifications.     

Pulsed-valve chemical ionization for gas chromatography/fourier-transform mass spectrometry

The pressure requirements for chemical ionization g.c./F.t.m.s. which restrict mass resolution and accuracy are overcome through use of a pulsed valve that provides momentary reagent gas pressures. For alternate electron impact (EI)/chemical ionization (c.i.) g.c./F.t.m.s., similar resolution for both e.i. and c.i. data is demonstrated. The efficiency of chemical ionization with the pulsed valve is similar to static high pressure c.i. measurements of several model compounds. Results from the analysis of peppermint oil and a fuel additive illustrate the potential information available from a single g.c./F.t.m.s. experiment.     

Classification of jet fuels by fuzzy rule-building expert systems applied to three-way data by fast gas chromatography--fast scanning quadrupole ion trap mass spectrometry

A fast method that can be used to classify unknown jet fuel types or detect possible property changes in jet fuel physical properties is of paramount interest to national defense and the airline industries. While fast gas chromatography (GC) has been used with conventional mass spectrometry (MS) to study jet fuels, fast GC was combined with fast scanning MS and used to classify jet fuels into lot numbers or origin for the first time by using fuzzy rule-building expert system (FuRES) classifiers. In the process of building classifiers, the data were pretreated with and without wavelet transformation and evaluated with respect to performance. Principal component transformation was used to compress the two-way data images prior to classification. Jet fuel samples were successfully classified with 99.8 ± 0.5% accuracy for both with and without wavelet compression. Ten bootstrapped Latin partitions were used to validate the generalized prediction accuracy. Optimized partial least squares (o-PLS) regression results were used as positively biased references for comparing the FuRES prediction results. The prediction results for the jet fuel samples obtained with these two methods were compared statistically. The projected difference resolution (PDR) method was also used to evaluate the fast GC and fast MS data. Two batches of aliquots of ten new samples were prepared and run independently 4 days apart to evaluate the robustness of the method. The only change in classification parameters was the use of polynomial retention time alignment to correct for drift that occurred during the 4-day span of the two collections. FuRES achieved perfect classifications for four models of uncompressed three-way data. This fast GC/fast MS method furnishes characteristics of high speed, accuracy, and robustness. This mode of measurement may be useful as a monitoring tool to track changes in the chemical composition of fuels that may also lead to property changes.     

Analysis of triacetone triperoxide by gas chromatography/mass spectrometry and gas chromatography/tandem mass spectrometry by electron and chemical ionization

The explosive triacetone triperoxide (TATP) has been analyzed by gas chromatography/mass spectrometry (GC/MS) and sub-nanogram detection limits are reported by ammonia positive ion chemical ionization (PICI), electron ionization (EI) and methane negative ion chemical ionization (NICI). Analysis by methane PICI and ammonia NICI gave detection limits in the low nanogram range. Analyses were carried out on (linear) quadrupole and ion trap instruments. Analysis of TATP by PICI using ammonia reagent gas is the preferred analytical method, producing low limits of detection as well as an abundant (greater than 60% of base peak) diagnostic adduct ion at m/z 240 corresponding to [TATP + NH4]+. Isolation of the [TATP + NH4]+ ion with subsequent collision-induced dissociation (CID) produces extremely low abundance product ions at m/z values greater than 60, and the m/z 223 ion corresponding to [TATP + H]+ was not observed. Density functional theory (DFT) calculations at the B88LYP/DVZP level indicate that dissociation of the complex to form NH4+ and TATP occurs at energies lower than peroxide bond dissociation, while protonation of TATP leads to cleavage of the ring structure. These results provide a method for pico-gram detection levels of TATP using commercial instrumentation commonly available in forensic laboratories. As a point of comparison, a detection limit of 15 ng was obtained by flame ionization detection.     

Determination of anabolic steroids by gas chromatography/negative-ion chemical ionization mass spectrometry and gas chromatography/negative-ion chemical ionization tandem mass spectrometry with heptafluorobutyric anhydride derivatization

A gas chromatography/mass spectrometry (GC/MS) method is described which uses negative ion chemical ionization (NCI) and tandem mass spectrometry (MS/MS) for the determination of eight anabolic steroids in human urine. Eight anabolic steroids were derivatized by heptafluorobutyric anhydride (HFBA), and were determined using GC/NCI-MS and GC/NCI-MS/MS. The linear correlation coefficients for calibration in NCI-MS/MS were in the range 0.9880-0.9988. This method of derivatization with HFBA for use with GC/NCI was useful in determinations of 19-norandrosterone, boldenone, 19-noretiocholanolone, 2-methylandrosterone, nandrolone, 1-methyleneandrosterone, 1-methylandrosterone, 4-dihydroboldenone and mesterolone. The detection limits of this procedure were 5-20 ppb at a signal-to-noise (S/N) ratio of 3.     

Supersonic gas chromatography/mass spectrometry

A new gas chromatography/mass spectrometry (GC/MS) system was designed and evaluated which we have named 'Supersonic GC/MS'. It is based on a modification of a commercially available GC/MS system to include a supersonic molecular beam (SMB) MS interface. In this system the standard electron ionization (EI) ion source was replaced with a fly-through EI ion source mounted in the path of the SMB. A hyperthermal surface ionization (HSI) ion source combined with a 90 degrees ion mirror (for the EI-produced ions) was also added, and placed inside the quadrupole mass analyzer in place of its original EI ion source. The 'Supersonic GC/MS' system requires 18 cm added bench space plus the addition of an air-cooled 60 L/s diffusion pump and a 537 L/min rotary pump. The system is user friendly since all the gas flow rates, heated zones, sampling and data analysis are performed the same way as the original system and are computer-controlled via the original software. Similar EI sensitivity was obtained as with the original system for hexachlorobenzene and octafluoronaphthalene, while improved EI detection limits were demonstrated for methyl stearate and eicosane due to the significant enhancement of their molecular ion abundances. A GC/MS detection limit of 500 ag for pyrene was demonstrated using HSI. Good supersonic expansion cooling was achieved with large alkanes, despite the use of a rotary pump at the nozzle chamber instead of a diffusion pump. High temperature GC/MS analysis was demonstrated for large polycyclic aromatic hydrocarbons (PAHs) including ovalene and decacyclene (ten rings). Library searches with EI mass spectra are demonstrated, and it is explained why the enhancement of the molecular ion actually improves the library search in most cases. The analysis of large phthalate esters is also described, and the improvement obtained is shown to originate from their enhanced molecular and high mass fragment ions.     

Long-term stability of a gas chromatography/mass spectrometry system in quantitative gas analysis

A gas chromatograph/quadrupole mass spectrometer (GC/MS) system was used to supervise a test programme for evaluating the potential of a natural gas storage plant. The dispersion characteristics of a large nitrogen reservoir located in a tight sandstone formation 1600 m below sea level between claystones, was investigated by injection and withdrawal of 350 000 m³ nitrogen with argon as tracer gas. The GC/MS system was installed in a shed in an open field and operated under computer control continuously 24 h a day for three weeks; about 3000 analyses were done. The on-line results were in good agreement with those obtained from additional gas samples withdrawn every 4 h for independent quantitative gas analyses with a purpose-built mass spectrometer.     

Early gas chromatography/mass spectrometry

Spectroscopy Laboratory, The Dow Chemical Company, Midland, Michigan, USA In December 1955 or thereabouts, the authors coupled a homemade gas chromatograph to a research time-of-flight mass spectrometer constructed by W. C. Wiley, I. H. McLaren, and D. B. Harrington. This unique gas chromatography/mass spectrometry (GC/MS) instrument generated mass spectra at a lo-kHz rate for display on an oscilloscope; eluted gas chromate graphic components, such as methanol, acetone, benzene, toluene, and carbon tetrachloride, could be visually identified immediately from the oscilloscope display. Many years of further research and development in many laboratories worldwide were necessary, however, to make continuous on-line GC/MS the uniquely valuable analytical tool that it is today.     

Combined gas chromatography/tandem mass spectrometry using laser photodissociation

Two fibre-optic interfaces were constructed for laser photodissociation/tandem mass spectrometry using an ion trap spectrometer. These interfaces allow sample introduction from a liquid reservoir, solids probe and gas chromatograph. The laser/ion trap configuration was applied to the analysis of a mixture of alkylbenenes separated by gas chromatography using 573 nm photons.     

Quantitative analysis of estrogens in human urine using gas chromatography/negative chemical ionisation mass spectrometry

A sensitive procedure for the determination of estrogens in urine has been developed, using enzymatic hydrolysis and ether extraction followed by capillary gas chromatography with negative chemical ionisation mass spectrometry (GC/NCI-MS) of the pentafluorobenzoyl derivatives. These derivatives were superior for GC/NCI-MS to trifluoroacetyl, heptafluorobutyl, pentadecafluorooctanoyl and perfluorotolyl derivatives, giving characteristic negative molecular ions as the base peak for each of the naturally occurring estrogens estrone, estradiol and estriol, and for the synthetic estrogen ethynylestradiol used in contraceptive pills. The method was also suitable for determination of some metabolites of estrone and estradiol. The specificity and sensitivity of the GC/NCI-MS method simplifies sample preparation. Recovery of spiked samples was in the range 84-101% for the natural estrogens based on additions to increase the concentration by 5 and 1 microg L(-1). The repeatability of the method was 1-8% for all estrogens.     

Quantitative analysis of phthalates using a pyrolyzer gas chromatography/mass spectrometry method

A pyrolyzer gas chromatography/mass spectrometry (GC/MS) method eliminates toxic solvents that burden our environment and can address the crucial problem of the solvent extraction GC/MS method. The purpose of this study is to establish an efficient quantitative analysis method for 10 phthalates that are regulated by the several governments. A change of concentrations over time for phthalates and internal standards was measured to verify the feasibility of using an auto sampler that facilitates analyzing multiple samples. Both standards maintained constant concentrations over the appropriate time for analysis. A certified reference material under the auspices of the Korea Research Institute of Standards and Science was used to verify the calibration curve obtained by the pyrolyzer GC/MS method, and a deviation was considered similar to the solvent extraction GC/MS method. Then, the limit of detection and limit of quantitation values were confirmed for various consumer products. To verify the reliability of the method, a comparative test with several accredited testing institutes was conducted, and the results were within the standard deviations of the results provided by the institutes. These results indicate that the pyrolyzer GC/MS method can be used in not only screening but also in accurate quantitative analysis.     

Analysis of 7-methylguanine using isotope dilution and gas chromatography/electron-capture negative chemical ionization mass spectrometry

This paper presents results obtained for in vivo endogenous and exogenous 7-methylguanine (7-MG) analyzed using a method incorporating gas chromatography with electron-capture negative chemical ionization mass spectrometry and isotope dilution (GC/EC-ID-MS). 13C4-Labeled 7-MG was synthesized to serve as an internal standard to improve accuracy of quantitation, and was used to analyze 7-MG in livers of control mice and dacarbazine-treated mice. The results confirm that 7-MG in tissue DNA can be measured using this GC/EC-ID-MS method with excellent sensitivity and specificity. Administration of 0, 30, and 60 mg/kg dacarbazine to mice led to dose-dependent increases in the formation of 7-MG. The results indicate that this method could be applied to the analysis of endogenous and exogenous 7-MG in human tissues for future molecular epidemiology studies on potential health effects caused by methylating agents.     

Detection of new propofol metabolites in human urine using gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry techniques

Using hyphenated analytical techniques, gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS), a study on minor propofol metabolites in human urine was conducted. These techniques allowed identification of two new phase I metabolites (2-(omega-propanol)-6-isopropylphenol and 2-(omega-propanol)-6-isopropyl-1,4-quinol). In addition, their four corresponding conjugates (three glucuronides and one sulphate) were detected. Thus in human urine at least eight conjugate metabolites are produced, derived from four different aglycones (propofol; 2, 6-diisopropyl-1,4-quinol; 2-(omega-propanol)-6-isopropylphenol and 2-(omega-propanol)-6-isopropyl-1,4-quinol).     

Metabolomic investigation of gastric cancer tissue using gas chromatography/mass spectrometry

Gastric cancer screening or diagnosis is mainly based on endoscopy and biopsy. The aim of this study was to identify the difference of metabolomic profile between normal and malignant gastric tissue, and to further explore tumor biomarkers. Chemical derivatization together with gas chromatography/mass spectrometry (GC/MS) was utilized to obtain the metabolomic information of the malignant and non-malignant tissues of gastric mucosae in 18 gastric cancer patients. Acquired metabolomic data was analyzed using the Wilcoxon rank sum test to find the tissue metabolic biomarkers for gastric cancer. A diagnostic model for gastric cancer was constructed using principal component analysis (PCA), and was assessed with receiver-operating characteristic (ROC) curves. Results showed that 18 metabolites were detected differently between the malignant tissues and the adjacent non-malignant tissues of gastric mucosa. Five metabolites were also detected differently between the non-invasive tumors and the invasive tumors. The diagnostic model could discriminate tumors from normal mucosae with an area under the curve (AUC) value of 0.9629, and another diagnostic model constructed for clinical staging was assessed with an AUC value of 0.969. We conclude that the metabolomic profile of malignant gastric tissue was different from normal, and that the selected tissue metabolites could probably be applied for clinical diagnosis or staging for gastric cancer.     

Quantitative gas chromatography/time-of-flight mass spectrometry: a review

Time-of-flight (TOF) instruments have recently gained popularity in quantitative analyses. Normally, TOF mass spectrometers are used for accurate mass measurements for empirical formula verification. However, over the past decade, they have been used quantitatively as well. Because of the fast separations and narrow peaks that result from gas chromatography separations, scanning mass spectrometers are not ideal detectors. TOF mass spectrometers, however, have the ability to collect spectra at a faster rate. Two-dimensional gas chromatography has also been introduced to further resolve peaks from complex matrices. Two-dimensional gas chromatography results in a faster separation as well as narrower peaks. This paper reviews the methods currently in the literature for the quantitation of compounds using one- and two-dimensional gas chromatography and TOF mass spectrometry detection.     

A single glucose derivative suitable for gas chromatography/mass spectrometry and gas chromatography/combustion/isotope ratio mass spectrometry

The incorporation of stable isotopes improves the assessment of glucose metabolism and, with some researchers using two tracers, (2)H-glucose assessed by gas chromatography/mass spectrometry (GC/MS) and (13)C-glucose by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS), a common derivative for both is advantageous. The most commonly used derivatives for GC/MS are inappropriate for GC/C/IRMS as additional functional groups dilute the label. We therefore considered the suitability of six derivatives for both GC/MS and GC/C/IRMS. Glucose alkylboronates were prepared by adding the appropriate alkylboronic acid (butyl- or methylboronic acid) in pyridine to desiccated glucose. The derivatisation was completed by reacting this with either (a) acetic anhydride or trifluoroacetic anhydride (acetate derivatives) or (b) bis(trimethylsilyl)trifluoroacetamide BSTFA (TMS derivatives). All six derivatives were assessed using GC/MS and (13)C GC/C/IRMS.Neither TMS derivative exhibited any signal intensity in the molecular ion, although a M-15 ion showed good agreement between experimental and theoretical data and, whilst still low in intensity, could be suitable for isotope work. Similarly, none of the acetate derivatives showed any intensity at the molecular ion although three key fragmentation series were identified. The most attractive sequence, initiated by the loss of 1,2 cyclic boronate, resulted in the main fragment ion of interest, m/z 240, corresponding to the fluorinated methylboronate derivate. Minimal carbon and hydrogen atoms are added to this derivative making it an excellent choice for stable isotope work, while proving suitable for analysis by both GC/MS and GC/C/IRMS.