化学计量学方法用于蛋白质组学质谱数据的特征筛选

提出了一种基于偏最小二乘判别分析和F-score的特征筛选方法,并将其用于蛋白质组学质谱数据分析。方法主要包含3个步骤:(1)用LIMPIC算法对原始数据进行预处理;(2)计算每个变量的F-score值并将所有变量按F-score值降底的顺序排列;(3)采用偏最小二乘判别分析交互检验按前向选择法选择最佳变量子集。用本方法对一组卵巢癌数据进行分析,最终从原始的15154个质荷比变量中选择了12个特征变量作为潜在生物标记物,它们在训练集上交叉检验的特异性和灵敏度分别为98.36%和98.15%,在独立测试集上的特异性和灵敏度分别为96.67%和100%。用筛选出的变量作PCA所得的结果显示这些变量能够较好地将样本分类,说明能够反映出样本的类别信息。所提出的方法可用于蛋白质组学质谱数据的特征筛选及样本分类。     

Complete profiling and characterization of in vitro nefazodone metabolites using two different tandem mass spectrometric platforms

This paper describes the complete profiling and characterization of in vitro metabolites of the antidepressant agent nefazodone (NEF) generated by human liver microsome (HLM). Two new metabolic pathways (biotransformation) for NEF have been discovered by the characterization of three new metabolites, including two new metabolites (M24, M25) formed due to the N-dealkylation reaction that occurred between the triazolone and propyl units, and one new metabolite (M26) formed due to the O-dearylation reaction that occurred on the phenoxyethyl unit. These metabolites were initially detected by a 4000 Q-Trap instrument and then confirmed by exact mass measurement using an LTQ-Orbitrap. Both instruments proved to be capable of providing complete in vitro metabolite information in a single liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis, although each had its advantages and disadvantages. One noticeable disadvantage of the 4000 Q-Trap was the reduced quality of isotopic pattern in the enhanced mass scan (EMS) spectrum when it was used as survey scan to trigger multiple dependent product ion scans. The problem was especially exacerbated for minor metabolites with low signal intensity. On the other hand, the LTQ-Orbitrap maintained excellent isotopic pattern when used as a full scan survey scan. Twenty-six metabolites were detected and identified. The formation of these new metabolites was also confirmed by analyzing duplicate incubations at different time points.     

Limitations of mass spectrometric methods for the characterization of polydisperse materials

This paper is a review of work on the characterization of coal liquids and petroleum residues and asphaltenes over several decades in which various mass spectrometric methods have been investigated. The limitations of mass spectrometric methods require exploration in order to understand what the different analytical methods can reveal about environmental pollution by these kinds of samples and, perhaps more importantly, what they cannot reveal. The application of mass spectrometry to environmental problems generally requires the detection and determination of the concentration of specific pollutants released into the environment by accident or design. The release of crude petroleum or coal liquids into the environment can be detected and tracked during biodegradation processes through specific chemicals such as alkanes or polyaromatic hydrocarbons (PAHs). However, petroleum asphaltenes are polydisperse materials of unknown mass range and chemical structures and, therefore, there are no individual chemicals to detect. It is necessary to determine methods of detection and the ranges of mass of such materials. This can only be achieved through fractionation to reduce the polydispersity of the initial sample. Comparison of mass spectrometric results with results from an independent analytical method such as size‐exclusion chromatography with a suitable eluent is advisable to confirm that all the sample has been detected and mass discrimination effects avoided. Copyright © 2010 John Wiley & Sons, Ltd.     

Structural characterization of hexoses and pentoses using lead cationization. An electrospray ionization and tandem mass spectrometric study

The analytical potential of the complexation of isomeric underivatized hexoses (D-glucose, D-galactose, D-mannose, D-talose, D-fructose), methylglycosides (1-O-methyl-alpha-D-glucose and 1-O-methyl-beta-D-glucose) and pentoses (D-ribose, D-xylose, D-arabinose and D-lyxose) by Pb(2+) ions, was investigated by electrospray ionization and tandem mass spectrometry (MS/MS). Pb(2+) ions react mainly with monosaccharides by proton abstraction to generate [Pb(monosaccharide)(m) - H](+) ions (m = 1-3). At low cone voltage, a less abundant series of doubly charged ions of general formula [Pb(monosaccharide)(n)](2+) is also observed. The maximum number n of monosaccharides surrounding a single Pb(2+) ion depends on the metal : monosaccharide ratio. Our study shows that MS/MS experiments have to be performed to differentiate Pb(2+)-coordinated monosaccharides. Upon collision, [Pb(monosaccharide) - H](+) species mainly dissociate according to cross-ring cleavages, leading to the elimination of C(n)H(2n)O(n) neutrals. The various fragmentation processes observed allow the C(1), C(2) and C(4) stereocenters of aldohexoses to be characterized, and also a clear distinction aldoses and fructose. Furthermore, careful analysis of tandem mass spectra also leads to successful aldopentose distinction. Lead cationization combined with MS/MS therefore appears particularly useful to identify underivatized monosaccharides.     

Multi-element characterization of silicon nitride powders by atomic and mass spectrometric solution methods

A sample pretreatment technique for silicon nitride involving digestion and matrix/traces separation was developed by means of radiotracers and applied to analysis of this material by inductively coupled plasma atomic emission spectrometry, inductively coupled plasma mass spectrometry and graphite furnace atomic absorption spectrometry. The results obtained for a high purity silicon nitride material by these methods are compared each with the other and with those obtained by neutron activation analysis. The limits of detection and the capabilities of the methods are compared and discussed.     

Structural characterisation of Baltic amber and its solvent extracts by several mass spectrometric methods

A sample of Baltic amber ( approximately 40 million yrs old) has been extracted using pentane, toluene and 1-methyl-2-pyrrolidinone (NMP). The relationship between solubility characteristics of the extracts in relation to molecular mass and chemical makeup has been investigated. The extracts were first characterised by (13)C-NMR spectrometry, size exclusion chromatography (SEC) and UV-fluorescence spectroscopy. The fractions differed less in terms of chemical structural features than they did in terms of molecular mass. This contrasts markedly with data on fractions of coal-derived liquids, but parallels results from petroleum-derived vacuum residues. In SEC, the toluene soluble/pentane insoluble fraction gave a peak for high mass material at about 67 000 u. Material excluded from the column porosity in this fraction and in NMP solubles eluted between 8 and 11 min, corresponding to polystyrene masses between 200 000 and several million u. A column with a larger pore size distribution was calibrated using polystyrene and polymethylmethacrylate standards with detection by a light-scattering evaporative analyser. The largest polystyrene standard (15.4 million u) eluted at 13.4 min, similar to that of the earliest eluting amber-derived material in the NMP solubles fraction. Results from probe-MS and pyrolysis-GC/MS have been used to confirm the similarity of chemical structures of the three solubility fractions. Broadly, low mass ions appear to correspond to the various monomeric units of structures present in the amber, the higher mass ions to dimer units and the molecular ions to the different combinations of three or more monomeric units. The main monomer groups have been identified in detail, showing a situation very different from that of coal-derived materials, where the sizes of aromatic ring systems increase with molecular size.     

Electrospray ionization tandem mass spectrometric and electron impact mass spectrometric characterization of mycosporine-like amino acids

Positive-ion mass spectral fragmentations of seven mycosporine-like amino acids (MAAs) are reported and discussed. The MAAs studied are small compounds composed of a cycloheximine ring substituted with amino acid or amino alcohol units. Techniques used include electron impact (EI) and electrospray ionization (ESI) with tandem mass spectrometry (MS/MS). ESI-MS/MS showed unusual small radical losses, generally resulting from the loss of a methyl group with the exception of shinorine and porphyra for which the initial losses were 30 and 44 Da, respectively. As expected from structural similarities, porphyra, shinorine and palythinol displayed similar fragmentation patterns, while palythenic acid and palythene fragmented in a similar manner. Overall, the ESI-MS/MS fragmentations at m/z <200 exhibited a distinctive pattern for all seven MAAs with characteristic ions at m/z 137, 168, 186, and 197 or 199. Several ions were observed for each of the MAAs analyzed, and together provide a useful and potentially diagnostic pattern for identification of MAAs and as an aid in structure elucidation of novel MAAs. For GC/EI-MS analysis, trimethylsilyl (TMS) derivatives were made. The EI-MS fragmentation patterns of TMS-MAAs showed many features typical of TMS-derivatized alpha-amines. The precursor TMS-MAA ion was not detected, but a [M-90](+ radical) ion was the highest-mass intense peak observed for palythine, palythinol and shinorine, while palythene gave a [M-116](+ radical) ion. Besides determining the number of acidic hydrogens, EI-MS of TMS-derivatized MAAs will aid in structure elucidation of novel MAAs.     

Mass spectrometric characterization of different norandrosterone derivatives by low-cost mass spectrometric detectors using electron ionization and chemical ionization

The abuse of nortestosterone in sport is an important problem in doping-control analysis. In order to detect the main urinary metabolite of nortestosterone, norandrosterone (NA), sensitive and specific methodology is necessary. In this context the use of a low-cost mass spectrometric detector such as the Finnigan MAT ion-trap detector (ITD) was studied. The electron ionization (EI) and positive-ion chemical ionization (PICI) mass spectra of the methoxime-trimethylsilyl, trimethylsilyl-enol trimethylsilyl ether and pentafluoropropionic ester derivatives of NA are described. The limits of detection of these derivatives are compared with those obtained by the Hewlett-Packard mass selective detector (MSD), another low-cost mass spectrometric detector and operating only in the EI mode. For the derivatives of the reference standard of NA the ITD has in the EI mode the same limit of detection, in the range of 0.5 to 1 ng injected on the column, as the MSD. However, under these conditions the ITD provides more spectrometric information, because it gives full scan data. Moreover, with the same or even improved limits of detection the ITD can operate in the PICI mode. On the other hand, for the analysis of NA isolated from urine samples, the performance of the MSD was better than that of the ITD. The ion trapping technique is probably limited when the chemical background is high.     

N-methyl-N-trimethylsilyltrifluoroacetamide-promoted synthesis and mass spectrometric characterization of deuterated ephedrines

Synthesis and mass spectrometric characterization of drugs or metabolites labeled by stable isotopes has been of great interest in fields of clinical, forensic and doping control analysis. Deuterated ephedrine and p-hydroxypseudoephedrine were prepared from corresponding amines by a novel procedure utilizing N- methyl-N-trimethylsilyltrifluoroacetamide and deuterated iodomethane. The mechanism of methylation was studied by mass spectrometry using phenylethylamine as a model compound, and a rearrangement based on an intermediate six-membered ring structure with a trimethylsilyl-enol-ether is proposed giving rise to a leaving group of trimethyliodosilane and the desired monomethylated product. Deuterated analogues to frequently quantitated ephedrines were readily synthesized with purities >90%, and mass spectra recorded under different ionization and dissociation conditions presented distinct fragmentation processes including eliminations of water and methylamine as well as the generation of a benzyl cation.     

Structural confirmation of ostreocin-D by application of negative-ion fast-atom bombardment collision-induced dissociation tandem mass spectrometric methods

Negative-ion fast-atom bombardment collision-induced dissociation tandem mass spectrometric (FAB-CID-MS/MS) methodology was successfully applied to verify the highly complex structure of ostreocin-D (MW 2633), a new palytoxin analog isolated from the marine dinoflagellate Ostreopsis siamensis and proposed to be 42-hydroxy-3,26-didemethyl-19,44-dideoxypalytoxin based on NMR data. The charge-remote fragmentations were facilitated by a negative charge introduced to a terminal amino group or to a hydroxyl group at the other terminus by a reaction with 2-sulfobenzoic acid cyclic anhydride. Product ions generated from the [M - H](-) ions provided information on the structural details of ostreocin-D. Comparisons between the spectral data for ostreocin-D and palytoxin also provided a rational basis for the assignments of product ions.     

A comparative analysis of gold-rich plant material using various analytical methods

During 2003 a field demonstration of gold phytoextraction technology was conducted in Brazil. As there is no commercially available biogeochemical standard reference material with an elevated concentration of gold, the trial biomass was analysed for its gold content using five analytical methods, at five laboratories, to confirm the concentration of gold in the harvested plant material. Nitric and hydrochloric acid digest followed by ICP-OES solution analysis of a doré bead prepared through fire assay of vegetative material was considered the benchmark analytical method to which the other results were compared. The gold concentrations reported by the five laboratories varied widely. Flame atomic absorption analysis of a solution prepared through the digest of plant ash by aqua regia proved the most accurate analytical method relative to fire assay. Gold concentrations reported by a New Zealand commercial laboratory using ICP-MS and a standard ‘biological materials digest’ procedure were affected by the digest method employed. X-ray fluorescence results may have been affected by synthetic standards that were prepared specifically for this investigation. Alternatively, matrix effects may not have been fully corrected for using XRF. Analysis of metal-rich biomass is becoming more common due to the popularity of studies that use plants to absorb heavy metals. The results of our comparative investigation emphasise that due care and consideration must be given to the selection of the analytical method chosen to analyse such plant material. Our results also highlight the need for standard reference materials that are suitably enriched in metals, such that these may be of use to phytoextraction studies.     

Depth profiling of sterically-stabilised polystyrene nanoparticles using laser ablation/ionisation mass spectrometric methods

An aerodynamic lens has been used to introduce polystyrene nanoparticles into an apparatus that combines laser vaporisation with mass spectrometric measurements of ion intensity. The particles have a mean diameter of 129 nm and are sterically-stabilised with poly(ethylene glycol) which coats the surface to a depth of approximately 5 nm. Measurements have been made at wavelengths of 266, 355, and 523 nm, and over a range of laser powers. The results provide clear evidence that depth profiling can be achieved by changing the wavelength of the ablating radiation, but that changes in power at a single wavelength have little influence on the range of ions observed. At 523 nm the mass spectra are predominantly derived from surface-bound material, whilst at 266 nm the dominant contribution is from ions related to the polystyrene core of the particles. It is proposed that these differences in behaviour can be equated with existing models of the laser ablation process.     

Quantification of triacylglycerol regioisomers in oils and fat using different mass spectrometric and liquid chromatographic methods

The regioisomers (sn-ABA/sn-AAB) of four triacylglycerols (TAGs), 18:2/18:2/18:1 (LLO), 18:2/18:1/18:1 (LOO), 16:0/18:1/18:1 (POO), and 16:0/16:0/18:1 (PPO), were quantified in lard, rapeseed oil, and sunflower seed oil by three different mass spectrometric methods using liquid chromatography (LC) and two different mass spectrometers. The ionization methods used were positive ion atmospheric pressure chemical ionization (APCI), positive ion electrospray ionization (ESI), and negative ion chemical ionization (NICI) with ammonia as the reagent gas. The LC/APCI-MS results with two different instrumentation types, LC/ESI-MS/MS and direct inlet ammonia NICI-MS/MS, were compared. The LC/APCI-MS method is based on the preferential formation of diacylglycerol (DAG) fragment ions during ionization by loss of sn-1/3 fatty acids from [M+H]+ ions. Similar formation of the DAG ions from [M+NH4]+ ions by collision-induced dissociation (CID) in the LC/ESI-MS/MS method and the [M-H--RCOOH-100]- ions from [M-H]- ions by CID in the direct inlet ammonia NICI-MS/MS method is observed. These methods were found to be useful and reliable in determining the regioisomeric structure of TAGs. No statistically significant differences were found between the results obtained with these methods. For LLO, LOO, and POO the proportions of sn-ABA isomer calculated from the results from all four methods were in rapeseed oil 7.7 +/- 6.5, 57.9 +/- 3.3, and 4.5 +/- 6.1%, respectively, and in sunflower seed oil 12.2 +/- 6.9, 34.0 +/- 5.2, and 1.4 +/- 2.8%, respectively. The proportions of ABA of POO and PPO in lard were 95.3 +/- 3.2 and 4.9 +/- 5.6%, respectively. This study also proved that the LC/APCI-MS/MS method examined is not applicable in the quantification of TAG regioisomers because the formation of DAG ions is not clearly dependent on the positional distribution of the fatty acids.     

Separation and identification of various vulcanization agents and antioxidants in two types of rubber by chromatographic and spectrometric methods

The aim of this study was to separate and identify by chromatographic and spectrometric methods, the various allergenic vulcanization agents and antioxidants used in the manufacture of industrial rubber. Specimens of elastomers were manufactured specially for this study. The specificity of the gas chromatographic method developed allows separation of all the manufacturing additives in the selected rubber types after one injection only, even though they belong to extremely varied chemical categories. The GLC method was coupled with mass spectrometry, which permitted identification of the peaks obtained and the study of the fragmentation of the 4 reference products under various conditions. Separation by TLC was performed in parallel on the same extracts, allowing rapid identification of the products tested for, and showed new spots after vulcanization.     

On-line high-performance liquid chromatography/mass spectrometric characterization of native oligosaccharides from glycoproteins

An on-line high-performance liquid chromatography/mass spectrometry (HPLC/MS) method is described for the rapid characterization of any type of oligosaccharide released from glycoproteins. The procedure can be applied without further manipulation to fractions collected from a high-performance anion-exchange chromatography-pulse amperometric detection (HPAEC-PAD) system commonly used for glycosylation mapping of glycoproteins, or to a pool of oligosaccharides directly released from glycoproteins. The system consists of a porous graphitized high-performance chromatography column (Hypercarb) coupled to a quadrupole time-of-flight (TOF) mass spectrometer. Oligosaccharides are eluted from the column with a gradient of ammonium acetate/acetonitrile and directly identified following in-source fragmentation. Some applications of the method are presented, as well as information about the spectra and fragmentation behavior observed for N- and O-linked oligosaccharides released from some recombinant glycoproteins. Low femtomole limits of detection are achieved using proper miniaturization.     

Calculation methods for direct internal mass fractionation correction of spiked isotopic ratios from multi-collector mass spectrometric measurements

It is difficult to do internal mass fractionation corrections for isotope dilution analysis by thermal ionization mass spectrometry (TIMS) or multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS), especially for MC-ICP-MS. In this study, calculation methods for direct internal fractionation correction of spiked isotope analysis by TIMS or MC-ICP-MS cycle by cycle for elements having at least two internal reference isotopic ratios are presented. For TIMS, direct internal mass fractionation correction calculation methods, based on both power and exponential laws, are derived; whereas for MC-ICP-MS, due to larger mass fractionation effects, only exponential law is considered. These calculation strategies can be applied for both static and multi-dynamic measurements. For multi-dynamic measurements, the isotope fractionation effect, gain and cup efficiency effects of different collectors, as well as ion beam fluctuation effects are all simultaneously eliminated. The calculation methods were verified by Sr isotopic analyses of spiked NBS987 standard solutions by TIMS and Hf isotopic analyses of spiked geological reference materials by MC-ICP-MS. In addition, precise and accurate calibrations of isotopic ratios of the spikes, based on the calculation methods, are discussed.     

The separation of arsenic species in soils and plant tissues by anion-exchange chromatography with inductively coupled mass spectrometry using various mobile phases

Anion-exchange chromatography (Hamilton, PRP-X100) with inductively coupled plasma mass spectrometry (ICP-MS) is commonly used for the speciation of arsenic in environmental and biological samples. However, retentions for As species are frequently different because of the use of widely different mobile phases. In addition, chloride in matrices interferes with arsenic determination. In this study, we systematically investigated various mobile phases based on ammonium salts affecting arsenic retention to eliminate chloride interference chromatographically. Hence, various mobile phases based on ammonium salts, including NH₄H₂PO₄, NH₄HPO₄, NH₄Ac, NH₄HCO₃ and NH₄NO₃, were examined for reasonable resolution and to separate chloride from arsenic species. The best result was obtained with a mobile phase containing 30 mM NH₄H₂PO₄ at pH 5.6, where the separation of arsenic species, including arsenite [As(III)], arsenate [As(V)], dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA)], was achieved within 9 minutes with reasonable resolution and free of chloride interference at its high level (500 mg L^− 1). The detection limits for the arsenic species were in the range of 0.1-0.3 μg L^− 1 with a direct injection of sample without removing matrix. Finally, the proposed method was used for the determination of arsenic species in contaminated soil and plant tissues.     

Quantitative characterization of differential ion suppression on liquid chromatography/atmospheric pressure ionization mass spectrometric bioanalytical methods

Ion suppression is a known phenomenon in atmospheric pressure ionization mass spectrometry. These suppression effects have been shown to adversely affect the accuracy and precision of quantitative bioanalytical methods. This paper presents a simple procedure for determining the impact of differential ion suppression on bioanalytical methods that utilize atmospheric pressure ionization mass spectrometric (APIMS) detection. This procedure was applied to the assessment of two potential internal standards, and to determine selectivity issues for another analyte which was to be measured in multiple species.