共查询到20条相似文献,搜索用时 15 毫秒
1.
Rojas-Cherto M Peironcely JE Kasper PT van der Hooft JJ de Vos RC Vreeken R Hankemeier T Reijmers T 《Analytical chemistry》2012,84(13):5524-5534
Multistage mass spectrometry (MS(n)) generating so-called spectral trees is a powerful tool in the annotation and structural elucidation of metabolites and is increasingly used in the area of accurate mass LC/MS-based metabolomics to identify unknown, but biologically relevant, compounds. As a consequence, there is a growing need for computational tools specifically designed for the processing and interpretation of MS(n) data. Here, we present a novel approach to represent and calculate the similarity between high-resolution mass spectral fragmentation trees. This approach can be used to query multiple-stage mass spectra in MS spectral libraries. Additionally the method can be used to calculate structure-spectrum correlations and potentially deduce substructures from spectra of unknown compounds. The approach was tested using two different spectral libraries composed of either human or plant metabolites which currently contain 872 MS(n) spectra acquired from 549 metabolites using Orbitrap FTMS(n). For validation purposes, for 282 of these 549 metabolites, 765 additional replicate MS(n) spectra acquired with the same instrument were used. Both the dereplication and de novo identification functionalities of the comparison approach are discussed. This novel MS(n) spectral processing and comparison approach increases the probability to assign the correct identity to an experimentally obtained fragmentation tree. Ultimately, this tool may pave the way for constructing and populating large MS(n) spectral libraries that can be used for searching and matching experimental MS(n) spectra for annotation and structural elucidation of unknown metabolites detected in untargeted metabolomics studies. 相似文献
2.
The coupling of microfabricated devices to nanoelectrospray mass spectrometers using both a triple quadrupole and a quadrupole time-of-flight mass spectrometer (QqTOF MS) is presented for the analysis of trace-level membrane proteins. Short disposable nanoelectrospray emitters were directly coupled to the chip device via a low dead volume connection. The analytical performance of this integrated device in terms of sensitivity and reproducibility was evaluated for standard peptide mixtures. A concentration detection limit ranging from 3.2 to 43.5 nM for different peptides was achieved in selected ion monitoring, thus representing a 10-fold improvement in sensitivity compared to that of microelectrospray using the same chip/mass spectrometer. Replicate injections indicated that reproducibility of migration time was typically less than 3.1% RSD whereas RSD values of 6-13% were observed on peak areas. Although complete resolution of individual components is not typically achieved for complex digests, the present chip capillary electrophoresis (chip-CE) device enabled proper sample cleanup and partial separation of multicomponent samples prior to mass spectral identification. Analyses of protein digests were typically achieved in less than 1.5 min with peak widths of 1.8-2.5 s (half-height definition) as indicated from individual reconstructed ion electropherograms. The application of this chip-CE/QqTOF MS system is further demonstrated for the identification of membrane proteins which form a subset of the Haemophilus influenzae proteome. Bands first separated by 1D-gel electrophoresis were excised and digested, and extracted tryptic peptides were loaded on the chip without any further sample cleanup or on-line adsorption preconcentration. Accurate molecular mass determination (< 5 ppm) in peptide-mapping experiments was obtained by introducing an internal standard via a postseparation channel. The analytical potential of this integrated device for the identification of trace-level proteins from different strains of H. influenzae is demonstrated using both peptide mass-fingerprint database searching and on-line tandem mass spectrometry. 相似文献
3.
Enders JR Marasco CC Kole A Nguyen B Sevugarajan S Seale KT Wikswo JP McLean JA 《IET systems biology》2010,4(6):416-427
The combination of microfluidic cell trapping devices with ion mobility-mass spectrometry offers the potential for elucidating in real time the dynamic responses of small populations of cells to paracrine signals, changes in metabolite levels and delivery of drugs and toxins. Preliminary experiments examining peptides in methanol and recording the interactions of yeast and Jurkat cells with their superfusate have identified instrumental set-up and control parameters and online desalting procedures. Numerous initial experiments demonstrate and validate this new instrumental platform. Future outlooks and potential applications are addressed, specifically how this instrumentation may be used for fully automated systems biology studies of the significantly interdependent, dynamic internal workings of cellular metabolic and signalling pathways. 相似文献
4.
The behavior of macromolecular systems at different temperatures is often crucial to their biological activity and function. While heat-induced changes of individual proteins are readily monitored by a number of spectroscopic methods, changes in noncovalent complexes of biomolecules are more challenging to interpret. Nanoelectrospray mass spectrometry is becoming increasingly powerful in the study of large noncovalent complexes, and here we describe the design, characterization, and application of a novel probe that allows the thermocontrol of the solution in the electrospray capillary. The transition temperature for the unfolding of the protein lysozyme is readily obtained and correlates closely with that measured by fluorescence spectroscopy, thereby demonstrating the validity of this approach. We apply this technique to the study of the 200-kDa complex of the small heat shock protein TaHSP16.9, revealing both its dissociation into suboligomeric species and an increase in its size and polydispersity at elevated temperatures. In contrast, gas-phase activation of this complex is also carried out and yields a dissociation pathway fundamentally different from that observed for thermal activation in solution. As such, this probe allows the study of the reversible heat-induced changes of noncovalent complexes in a biologically relevant manner. 相似文献
5.
Quantitative determination of noncovalent binding interactions using automated nanoelectrospray mass spectrometry 总被引:3,自引:0,他引:3
Electrospray ionization mass spectrometry (ESI-MS) has proven to be an extremely powerful tool for studying biomolecular structures and noncovalent interactions. Here we report a method using a fully automated, chip-based nanoESI-MS system to determine the dissociation constants (Kd) for the complexes of two different proteins with their ligands. The automated nanoelectrospray system, consisting of the NanoMate and ESI chip, serves functionally as a combination of autosampler and nanoelectrospray ionization source. This system provides all the advantages of conventional nanoelectrospray plus automated, high-throughput analyses without carryover. The automated nanoESI system was used to investigate quantitative noncovalent interactions between ribonuclease A (RNase A) and cytidylic acid ligands (2'-CMP, CTP), a well-characterized model protein-ligand complex, and between an inactive endocellulase mutant (Thermobifida fusca Cel6A D117Acd) and four oligosaccharide ligands (cellotriose, cellotetraose, cellopentaose, cellohexaose). Both titration and competitive binding approaches were performed prior to automated nanoESI-MS analysis with a Q-TOF mass spectrometer. Dissociation constants for each complex were calculated from the sum of ion peak areas of free and complexed proteins during the titration and competition experiments. The measured Kd values for the RNase A-CMP and Cel6A D117Acd-G3 complexes were found to be in excellent agreement with the available published values obtained by standard spectroscopic titration techniques. To our knowledge, this is the first report of using an ESI-MS approach to study the interactions between a cellulase and oligosaccharides. The results provide new insights for understanding the nature of cellulase-cellulose interactions. 相似文献
6.
Lin F Waag RC 《IEEE transactions on ultrasonics, ferroelectrics, and frequency control》2002,49(6):739-755
A common random input filter model is described for estimation and correction of wavefront aberration in ultrasonic b-scan imaging. In the model, aberration between the focus and the transducer elements is represented by the response of a linear filter bank to a common random signal. The response of each filter in the bank is found using a two-level extension of an existing subspace method for blind system identification. The receive waveforms are compensated using an inverse filter, and the transmit waveforms are predistorted using time reversal. To test the model, experiments were conducted using a two-dimensional array system to obtain echoes from a point reflector and from a random medium in each case through an aberrator. The aberrator is a phantom that mimics wavefront distortion produced by human abdominal wall, and the random medium is made to mimic ultrasonic characteristics of human liver. The results indicate the method can improve both the transmit and the receive focus and can outperform time-shift estimation and compensation as well as the method of backpropagation followed by time-shift estimation and compensation 相似文献
7.
A methodology is presented to identify parameters of non-linear models of excitation systems (ESs). Based on the use of genetic algorithms (GAs), the proposed methodology carries out simultaneous parameter identification of linear and non-linear model components. The computational algorithm allows to adequately identify model parameters and it is not affected by the noise present in the measurements. The application of this methodology was developed to identify and validate ES models of different technologies that are used in stability studies through dynamic simulations. First, model parameters of DC1A and ST1A type ES were determined in a simulation environment. The performance of two identifiers based on a GA paradigm is analysed: GA with arithmetic and intermediate recombination operators (GA-BASE) and GA based on differential evolution (GA-DE) mutation. Then the GA-DE identifier is applied to estimate parameters of a static ES (EXE) model of a Brazilian hydro power plant utilising measurements corrupted by noise and registered during field tests. The results obtained are satisfactory and the responses of the identified models are close to real system measurements. 相似文献
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State-of-the-art analytical methods for arsenic speciation rely typically on the availability of standards of defined structure, limiting the applicability of such methods to the determination of known compounds. Our previous high-energy tandem mass spectrometric studies demonstrated the strength of mass spectrometry for generating structurally diagnostic ions that allow for the identification of arsenic-containing ribofuranosides (arsenosugars) without the use of standards. We now report a more widely applicable and more sensitive approach, using negative-ion nano-electrospray low-energy tandem mass spectrometry for the generation of structurally useful product ions that allow for identification of arsenosugars at the picogram level. In the negative-ion mode, numerous product ions, suitable for characterizing naturally occurring dimethylated arsenosugars, were generated in high abundance. Application of the method to an algal extract unequivocally demonstrated the presence of a single dimethylated arsenosugar. In the positive-ion mode, characteristic tandem mass spectra were obtained for four trimethylarsonioribosides, allowing their identification without the need for standards. Overall it was demonstrated that nano-ES-MS/MS techniques can be used for characterizing arsenosugars on a routine basis, a necessary requirement for assessing potential health risks associated with consuming foods containing elevated levels of arsenosugars and for improving our understanding of arsenic biochemistry. 相似文献
10.
Current nano-LC/MS systems require the use of an enrichment column, a separation column, a nanospray tip, and the fittings needed to connect these parts together. In this paper, we present a microfabricated approach to nano-LC, which integrates these components on a single LC chip, eliminating the need for conventional LC connections. The chip was fabricated by laminating polyimide films with laser-ablated channels, ports, and frit structures. The enrichment and separation columns were packed using conventional reversed-phase chromatography particles. A face-seal rotary valve provided a means for switching between sample loading and separation configurations with minimum dead and delay volumes while allowing high-pressure operation. The LC chip and valve assembly were mounted within a custom electrospray source on an ion-trap mass spectrometer. The overall system performance was demonstrated through reversed-phase gradient separations of tryptic protein digests at flow rates between 100 and 400 nL/min. Microfluidic integration of the nano-LC components enabled separations with subfemtomole detection sensitivity, minimal carryover, and robust and stable electrospray throughout the LC solvent gradient. 相似文献
11.
Shen Y Zhao R Berger SJ Anderson GA Rodriguez N Smith RD 《Analytical chemistry》2002,74(16):4235-4249
We describe high-efficiency (peak capacities of approximately 10(3)) nanoscale (using column inner diameters down to 15 microm) liquid chromatography (nanoLC)/low flow rate electrospray (nanoESI) mass spectrometry (MS) for the sensitive analysis of complex global cellular protein enzymatic digests (i.e., proteomics). Using a liquid slurry packing method with carefully selected packing solvents, 87-cm-length capillaries having inner diameters of 14.9-74.5 microm were successfully packed with 3-microm C18-bonded porous (300-A pores) silica particles at a pressure of 18,000 psi. With a mobile-phase delivery pressure of 10,000 psi, these packed capillaries provided mobile-phase flow rates as low as approximately 20 nL/min at LC linear velocities of approximately 0.2 cm/s, which is near optimal for separation efficiency. To maintain chromatographic efficiency, unions with internal channel diameters as small as 10 microm were specially produced for connecting packed capillaries to replaceable nanoESI emitters having orifice diameters of 2-10 microm (depending on the packed capillary dimensions). Coupled on-line with a hybrid-quadrupole time-of-flight MS through the nanoESI interface, the nanoLC separations provided peak capacities of approximately 10(3) for proteome proteolytic polypeptide mixtures when a positive feedback switching valve was used for quantitatively introducing samples. Over a relatively large range of sample loadings (e.g., 5-100 ng, and 50-500 ng of cellular proteolytic peptides for 14.9- and 29.7-microm-i.d. packed capillaries, respectively), the nanoLC/nanoESI MS response for low-abundance components of the complex mixtures was found to increase linearly with sample loading. The nanoLC/nanoESI-MS sensitivity also increased linearly with decreasing flow rate (or approximately inversely proportional to the square of the capillary inner diameter) in the flow range of 20-400 nL/min. Thus, except at the lower loadings, decreasing the separation capillary inner diameter has an effect equivalent to increasing sample loading, which is important for sample-limited proteomic applications. No significant effects on recovery of eluting polypeptides were observed using porous C18 particles with surface pores of 300-A versus nonporous particles. Tandem MS analyses were also demonstrated using the high-efficiency nanoLC separations. Chromatographic elution time, MS response intensity, and mass measurement accuracy was examined between runs with a single column (with a single nanoESI emitter), between different columns (same and different inner diameters with different nanoESI emitters), and for different samples (various concentrations of cellular proteolytic peptides) and demonstrated robust and reproducible sensitive analyses for complex proteomic samples. 相似文献
12.
Baumann A Faust A Law MP Kuhlmann MT Kopka K Schäfers M Karst U 《Analytical chemistry》2011,83(13):5415-5421
Radioligands, which specifically bind to a receptor or enzyme (target), enable molecular imaging of the target expression by positron emission tomography (PET). One very promising PET tracer is (S)-1-(4-(2-[(18)F]-fluoroethoxy)benzyl)-5-[1-(2-methoxymethylpyrrolidinyl)sulfonyl]isatin (isatin), a caspase-3 inhibitor, which has been developed at the University Hospital of Mu?nster to image cell death (apoptosis). The translation of this novel tracer from preclinical evaluation to clinical examinations requires biodistribution studies, which characterize the pharmakodynamics and metabolic fate of the compound. This information is used to further optimize the radioligands and to interpret radioactive signals from tissues upon injection of the radioligand in vivo with respect to their specificity. The analysis of the metabolism of radioligands is hampered by the low amount of the compound being typically injected (nano/picomolar amount per injection). In the present study, electrochemistry (EC) is applied to elucidate the oxidative metabolism pathway of the radiotracer. Previous studies have demonstrated that EC can be utilized as a complementary tool to conventional in vitro approaches in drug metabolism studies. Thereby, potential oxidative metabolites of the isatin are determined by EC coupled to electrospray ionization mass spectrometry (EC/ESI-MS). Moreover, using EC/liquid chromatography (LC) and ESI-ion trap MS(n), structural elucidation of the oxidation products is performed. Comparatively to EC, in vitro metabolism studies with rat liver microsomes are conducted. Finally, the developed LC/ESI-MS method is applied to determine metabolites in body fluids and cell extracts from in vivo studies with the nonradioactive ((19)F) and radioactive isatin ((18)F). On the basis of the electrochemically generated oxidation products of the radioligand, the major radioactive metabolite occurring in vivo was successfully identified. 相似文献
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Quantitative bioanalysis by direct nanoelectrospray infusion coupled to tandem mass spectrometry has been achieved using an automated liquid sampler integrated with an array of microfabricated electrospray nozzles allowing rapid, serial sample introduction (1 min/ sample). Standard curves prepared in human plasma for verapamil (r2 = 0.999) and its metabolite norverapamil (r2 = 0.998) were linear over a range of 2.5-500 ng/ mL. Based on the observed precision and accuracy, a lower limit of quantitation of 5 ng/mL was assigned for both analytes. Sample preparation consisted of protein precipitation with an organic solvent containing the structural analogue gallopamil as an internal standard. Protein precipitation was selected both to maximize throughput and to test the robustness of direct nanoelectrospray infusion. Aliquots of supernatant (10 pL) were transferred to the back plane of the chip using disposable, conductive pipet tips for direct infusion at a flow rate of 300 nL/min. Electrospray ionization occurred from the etched nozzles (30-microm o.d.) on the front of the chip, initiated by a voltage applied to the liquid through the pipet tip. The chip was positioned near the API sampling orifice of a triple quadrupole mass spectrometer, which was operated in selected reaction monitoring mode. Results are presented that document the complete elimination of system carry-over, attributed to lack of a redundant fluid path. This technology offers potential advantages for MS-based screening applications in drug discovery by reducing the time for methods development and sample analysis. 相似文献
15.
Assembly tolerance analysis involves the determination of tolerances of critical dimensions. This paper addresses two basic areas in tolerance analysis and allocation. (1) Dimension normalization, which identifies the relevant functional dimensions. A new algorithm called the dimension block diagram (DBD) algorithm for dimension normalization is presented. (2) Dimension representation, which provides a robust framework for representing the tolerance chain. A new dimension representation framework using Assembly Dimensional Tolerance (ADT) tree is presented. The two methodologies are automated and integrated within the framework of a CAD system using an Expert System. A computer test bed software has been developed demonstrating the viability of this approach. 相似文献
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An integrated database and expert system has been developed for assisting the human analyst in identifying the failure mechanism of mechanical components. The system comprises six major modules: database and management system; case maintenance; knowledge acquisition and editing; expert system; explanation and test-recommendation facilities, and user interface. The knowledge acquisition and editing module has been detailed in Part I of a two-part paper [6]. The overall system and the details of other modules are described here. The system has been implemented using the M4 expert system shell, Microsoft Access database software, and Visual Basic. Illustrative examples are used to show the capability of the system. Also reported are the results obtained from four different tests to determine the system performance. 相似文献
18.
We demonstrate an approach for multianalyte chemical identification and quantitation using a single conventional radio frequency identification (RFID) tag that has been adapted for chemical sensing. Unlike other approaches of using RFID sensors, where a special tag should be designed at a much higher cost, we utilize a conventional RFID tag and coat it with a chemically sensitive film. As an example, we demonstrate detection of several vapors of industrial, health, law enforcement, and security interest (ethanol, methanol, acetonitrile, water vapors) with a single 13.56-MHz RFID tag coated with a solid polymer electrolyte sensing film. By measuring simultaneously several parameters of the complex impedance from such an RFID sensor and applying multivariate statistical analysis methods, we were able to identify and quantify several vapors of interest. With a careful selection of the sensing film and measurement conditions, we achieved parts-per-billion vapor detection limits in air. These RFID sensors are very attractive as ubiquitous multianalyte distributed sensor networks. 相似文献
19.
In the remanufacturing/manufacturing (R/M) integrated supply chain, the decisions of the manufacturer, the wholesaler, the retailer, the parts producer, the raw materials supplier, the collector, and the disassembly centre are interactional. In this paper, a system dynamics model is proposed to examine the long-term behaviour of the R/M integrated supply chain with reuse, remanufacturing, and recycling. The optimal decision sets of the remanufacturing ratio and the setup period of remanufacturing (r) are given, the joint decisions of all members of R/M integrated supply chain under optimal r are presented by the simulation results, and the impacts of optimal r on the joint decisions are analysed. 相似文献
20.
The quality traceability of precast components has largely affected the widespread adoption of prefabricated buildings. Blockchain technology provides an effective solution to change the centralized storage mode of traditional traceability system and its related disadvantages. In this paper, we propose a framework of quality traceability system for precast components based on blockchain technology. The system framework adopts a hybrid blockchain architecture and dual storage mode, defines three types of smart contracts, and creates an interactive and efficient source tracing query method, which could effectively achieve the goals of decentralization, openness, and non-tamperability, as well as efficient traceability. 相似文献