Ion Fusion Research Articles

Comprehensive Strategy to Construct In-House Database for Accurate and Batch Identification of Small Molecular Metabolites.

Identification of the metabolites is an essential step in metabolomics study to interpret the regulatory mechanism of pathological and physiological processes. However, it is still difficult in LC-MS n-based studies because of the complexity of mass spectrometry, chemical diversity of metabolites, and deficiency of standards database. In this work, a comprehensive strategy is developed for accurate and batch metabolite identification in nontargeted metabolomics studies. First, a well-defined procedure was applied to generate reliable and standard LC-MS2 data, including tR, MS1, and MS2 information at a standard operational procedure. An in-house database including about 2000 metabolites was constructed and used to identify the metabolites in nontargeted metabolic profiling by retention time calibration using internal standards, precursor ion alignment and ion fusion, auto-MS2 information extraction and selection, and database batch searching and scoring. As an application example, a pooled serum sample was analyzed to deliver the strategy, and 202 metabolites were identified in the positive ion mode. It shows our strategy is useful for LC-MS n-based nontargeted metabolomics study.

Enhanced MS/MS coverage for metabolite identification in LC-MS-based untargeted metabolomics by target-directed data dependent acquisition with time-staggered precursor ion list

Metabolite identification is one of the major bottlenecks in liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics owing to the difficulty of acquiring MS/MS information of most metabolites detected. Data dependent acquisition (DDA) has been currently used to acquire MS/MS data in untargeted metabolomics. When dealing with the complex biological samples, top-n-based DDA method selects only a small fraction of the ions for fragmentation, leading to low MS/MS coverage of metabolites in untargeted metabolomics. In this study, we proposed a novel DDA method to improve the performance of MS/MS acquisition in LC-MS-based untargeted metabolomics using target-directed DDA (t-DDA) with time-staggered precursor ion lists (ts-DDA). Full scan-based untargeted analysis was applied to extract the target ions. After peak alignment, ion filtration, and ion fusion, the target precursor ion list was generated for subsequent t-DDA and ts-DDA. Compared to the conventional DDA, the ts-DDA exhibits the better MS/MS coverage of metabolomes in a plasma sample, especially for the low abundant metabolites. Even in high co-elution zones, the ts-DDA also showed the superiority in acquiring MS/MS information of co-eluting ions, as evidenced by better MS/MS coverage and MS/MS efficiency, which was mainly attributed to the pre-selection of precursor ion and the reduced number of concurrent ions. The newly developed method might provide more informative MS/MS data of metabolites, which will be helpful to increase the confidence of metabolite identification in untargeted metabolomics.

An improved pseudotargeted metabolomics approach using multiple ion monitoring with time-staggered ion lists based on ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry

Pseudotargeted metabolomics is a novel strategy integrating the advantages of both untargeted and targeted methods. The conventional pseudotargeted metabolomics required two MS instruments, i.e., ultra-high performance liquid chromatography/quadrupole-time- of-flight mass spectrometry (UHPLC/Q-TOF MS) and UHPLC/triple quadrupole mass spectrometry (UHPLC/QQQ-MS), which makes method transformation inevitable. Furthermore, the picking of ion pairs from thousands of candidates and the swapping of the data between two instruments are the most labor-intensive steps, which greatly limit its application in metabolomic analysis. In the present study, we proposed an improved pseudotargeted metabolomics method that could be achieved on an UHPLC/Q-TOF/MS instrument operated in the multiple ion monitoring (MIM) mode with time-staggered ion lists (tsMIM). Full scan-based untargeted analysis was applied to extract the target ions. After peak alignment and ion fusion, a stepwise ion picking procedure was used to generate the ion lists for subsequent single MIM and tsMIM. The UHPLC/Q-TOF tsMIM MS-based pseudotargeted approach exhibited better repeatability and a wider linear range than the UHPLC/Q-TOF MS-based untargeted metabolomics method. Compared to the single MIM mode, the tsMIM significantly increased the coverage of the metabolites detected. The newly developed method was successfully applied to discover plasma biomarkers for alcohol-induced liver injury in mice, which indicated its practicability and great potential in future metabolomics studies.

Multiple reaction monitoring-ion pair finder: a systematic approach to transform nontargeted mode to pseudotargeted mode for metabolomics study based on liquid chromatography-mass spectrometry.

Pseudotargeted metabolic profiling is a novel strategy combining the advantages of both targeted and untargeted methods. The strategy obtains metabolites and their product ions from quadrupole time-of-flight (Q-TOF) MS by information-dependent acquisition (IDA) and then picks targeted ion pairs and measures them on a triple-quadrupole MS by multiple reaction monitoring (MRM). The picking of ion pairs from thousands of candidates is the most time-consuming step of the pseudotargeted strategy. Herein, a systematic and automated approach and software (MRM-Ion Pair Finder) were developed to acquire characteristic MRM ion pairs by precursor ions alignment, MS(2) spectrum extraction and reduction, characteristic product ion selection, and ion fusion. To test the reliability of the approach, a mixture of 15 metabolite standards was first analyzed; the representative ion pairs were correctly picked out. Then, pooled serum samples were further studied, and the results were confirmed by the manual selection. Finally, a comparison with a commercial peak alignment software was performed, and a good characteristic ion coverage of metabolites was obtained. As a proof of concept, the proposed approach was applied to a metabolomics study of liver cancer; 854 metabolite ion pairs were defined in the positive ion mode from serum. Our approach provides a high throughput method which is reliable to acquire MRM ion pairs for pseudotargeted metabolomics with improved metabolite coverage and facilitate more reliable biomarkers discoveries.

Ion Fusion of High-Resolution LC–MS-Based Metabolomics Data to Discover More Reliable Biomarkers

A systematic approach for the fusion of associated ions from a common molecule was developed to generate "one feature for one peak" metabolomics data. This approach guarantees that each molecule is equally selected as a potential biomarker and may largely enhance the chance to obtain reliable findings without employing redundant ion information. The ion fusion is based on low mass variation in contrast to the theoretical calculation measured by a high-resolution mass spectrometer, such as LTQ orbitrap, and a high correlation of ion pairs from the same molecule. The mass characteristics of isotopic distribution, neutral loss, and adduct ions were simultaneously applied to inspect each extracted ion in the range of a predefined retention time window. The correlation coefficient was computed with the corresponding intensities of each ion pair among all experimental samples. Serum metabolomics data for the investigation of hepatocellular carcinoma (HCC) and healthy controls were utilized as an example to demonstrate this strategy. In total, 609 and 1084 ion pairs were respectively found meeting one or more criteria for fusion, and therefore fused to 106 and 169 metabolite features of the datasets in the positive and negative modes, respectively. The important metabolite features were separately discovered and compared to distinguish the HCC from the healthy controls using the two datasets with and without ion fusion. The results show that the developed method can be an effective tool to process high-resolution mass spectrometry data in "omics" studies.

Nuclear structure and dynamics from heavy - ion induced fission reactions

The study of heavy - ion fusion and fission reactions at near - barrier energies continues to be a rich source of information as regards nuclear structure and dynamics. From a comprehensive statistical model analysis of the fusion and the fission data including information on the pre - scission neutrons, for a large number of compound nuclei with masses around 200, it has been possible to determine reliably the fission barrier, the nuclear moment of inertia and the shell correction at the saddle point. Interestingly, it is found that for the nuclei in the mass region around 200, a significantly large fraction of the ground state shell correction persists at the deformed saddle - point. Systematic measurements of the fission fragment angular distributions spanning a range of projectiles with A = 9 to 19, bombarding the Th,U and Np targets have clearly brought out role of the entrance channel dynamics involving a new type of non - equilibrium fission, which we call pre - equilibrium fission comempeting with the equilibrium compound nucleus fission. A new model which takes into account the deformation and the spin values of the target and the projectile, the orientation and the entrance channel mass asymmetry dependence of the interacting nuclei has been developed which provides a good description of the fission fragment angular distribution data both at above and below barrier energies.

Multidimensional Langevin approach to description of near-barrier heavy-ion fusion and deep-inelastic collisions

A six-dimensional Langevin approach is developed for the analysis of near-barrier heavy- ion fusion and deep-inelastic collisions. In its framework, vibrational and rotational degrees of freedom of both nuclei are taken into account explicitly. Calculated fusion cross sections, compound nuclei spin distributions, and angular and energy distributions of deep-inelastic products showsatisfactory agreement with experimental data. c � 2003 MAIK "Nauka/Interperiodica". Fokker-Planck and Langevin equations may be successfully applied for the description of low-energy fusion and deep-inelastic collisions. These equations are based on the concepts of nuclear friction and stochastic behavior of the system with many degrees of freedom. The solution of the Langevin equations is less difficult compared to the Fokker-Planck equa- tion and does not require additional simplifying as- sumptions. It is well known that the deformations of nuclear surfaces and the rotation of deformed nuclei seriously affect the dynamics of nuclear interaction. Therefore, taking them into account is important for the description of low-energy nucleus-nucleus colli- sions. But this dramatically increases the calculation time and difficulty, which is the main reason why up to nowonly tw o- or four-dimensional calculations have been performed (1). In the present work, vibra- tional and rotational degrees of freedom of both nuclei are taken into account explicitly in the framework of the six-dimensional Langevin approach. Fusion cross sections, compound nuclei spin distributions, and angular and energy distributions of deep-inelastic products are calculated and compared with experi- mental data.

Lcritdeduced from fragment angular distributions inHe4-ion-induced fission

The published fragment anisotropy data in the fission of /sup 209/Bi induced by 23--140 MeV /sup 4/He ions are analyzed to deduce l/sub crit/ for different bombarding energies. These values of l/sub crit/ are found to be significantly lower than the optical model values of l/sub max/ at higher bombarding energies. The theoretical values of l/sub crit/ based on trajectory calculations with proximity potential and one body friction formalism are seen to agree with the experimentally deduced values. The significance of the above analysis for alternative experimental determination of /sup 4/He ion fusion (compound nucleus formation) cross section through deduction of l/sub crit/ is also pointed out.

Thermodynamic investigation of the shock adiabat

In in te rpre t ing exper imenta l data on the dynamic compress ib i l i t y of sol ids and l iquids, it is usual to assume, if this has not a l ready been determined exper imenta l ly , that the quantity 5 = sign (~p/~T)v is everywhere posi t ive [1, 2] {p is p r e s s u r e , T absolute t empera tu re , and V specif ic volume). However, there is no bas i s for assuming that the appearance of negative 5 in some regions Of p and T is improbable [3]. It is the re fore of i n t e re s t to invest igate the p ro pe r t i e s of the shock adiabat when the sign of 6 is va r i ab le . This is the f i r s t bas ic task of the p resen t study. In the p re sence of a phase t rans i t ion the shock adiabat exper iences a discontinuity at the co r responding point [2, 4, 5]. The re la t ion between the d i rec t ion of this discontinui ty and the thermodynamic p rope r t i e s of the ma te r i a l was found for a pa r t i cu l a r case in [6]. In that paper of the two poss ib le d i rec t ions of phase t rans i t ionfus ion and c rys t a l l i za t ion -on ly the fo r mer was examined, the condition of subsonic motion behind the shock wave being assumed valid for a l l points of the shock adiabat in the region of the d iscont inuity [1, 2]. The second bas ic task of the p re sen t study is to genera l ize these r e su l t s . At the same t ime, the known conclusions [1, 2] concerning the re la t ions between the i sent rope , the shock adiabat , and the Michelson line a re obtained in more genera l and compact form. Whereas in the general invest igat ion no l imi ta t ions , apa r t f rom the conditions of thermodynamic equil i b r ium [7], a r e imposed on the equation of s ta te , and the shock adiabat is r ega rded as one of the the rmodynamic curves i r r e s p e c t i v e of i ts r e l a t ionsh ip with the shock wave, in the analyzed examples conditions a r e assumed that pe rmi t an at l eas t qual i ta t ive expe r imen ta l de te rmina t ion of the shock adiabat in shock exper iments . We wil l cons ider some p rope r t i e s of the equil ib r ium equation of s ta te of a s ingle-component sy s t em