The local collision probability approximation (LCPA) method is introduced to compute molecular momentum transfer cross sections for comparison to ion mobility experiments. The LCPA replaces the ...(non-local) scattering trajectory used in the trajectory method to describe the collision process by a (local) collision probability function. This momentum transfer probability is computed using the exact same analyte-buffer interaction potential as used in the trajectory method. Subsequently, the momentum transfer cross section ΩLCPA(T) is calculated in a projection-type manner (corrected for shape effects through a shape factor). Benchmark calculations on a set of 208 carbon clusters with a range of molecular size and degree of concavity demonstrate that LCPA and trajectory calculations agree closely with one another. The results discussed here indicate that the LCPA is suitable to efficiently calculate momentum transfer cross sections for use in ion mobility spectrometry in conjunction with different buffer gases.
•Equation of motion for ions in non-uniform and dynamic electric fields under the influence of non-stationary buffer gases.•Direct determination of ion mobilities from measurements conducted in ...trapping ion mobility spectrometry (TIMS).•Results show that relative ion mobilities are currently directly amenable from TIMS experiments.
The feasibility of determining ion mobilities from measurements conducted in non-stationary buffer gases and in the presence of dynamic and non-uniform electric fields is examined theoretically and experimentally. First, an equation of motion of an ion ensemble is derived on the basis of a solution to the Boltzmann transport equation. Subsequently, this equation of motion is applied to derive the relationship between ion mobility and arrival time for the conditions present in an ion mobility drift tube and a trapped ion mobility spectrometry (TIMS) apparatus. Finally, the theoretical analysis is tested by determining the ion mobility of compounds present in an ESI tune mix directly from experimental TIMS data. Comparison to ion mobilities measured on a drift tube shows that relative ion mobilities are currently directly amenable from TIMS experiments. The analysis further suggests that absolute ion mobilities are, in principle, directly amenable from ion mobility measurements performed with non-stationary buffer gases and non-uniform and dynamic electric fields.
Data Fusion BLEIHOLDER, Jens; NAUMANN, Felix
ACM computing surveys,
01/2009, Letnik:
41, Številka:
1
Journal Article
Recenzirano
The development of the Internet in recent years has made it possible and useful to access many different information systems anywhere in the world to obtain information. While there is much research ...on the integration of heterogeneous information systems, most commercial systems stop short of the actual integration of available data. Data fusion is the process of fusing multiple records representing the same real-world object into a single, consistent, and clean representation.
This article places data fusion into the greater context of data integration, precisely defines the goals of data fusion, namely, complete, concise, and consistent data, and highlights the challenges of data fusion, namely, uncertain and conflicting data values. We give an overview and classification of different ways of fusing data and present several techniques based on standard and advanced operators of the relational algebra and SQL. Finally, the article features a comprehensive survey of data integration systems from academia and industry, showing if and how data fusion is performed in each.
Ion mobility spectrometry-mass spectrometry offers the potential to characterize structures of transient protein assemblies and protein isoforms by means of their orientationally-averaged momentum ...transfer cross-sections. A commonly observed phenomenon is the compaction of a protein in the ion mobility measurement, that is, the cross section measured for the protein by ion mobility spectrometry is smaller than the cross section expected for its native structure. Consequently, this compaction means that at least some structural changes of the protein must have occurred during the ion mobility measurement. A major challenge is then to identify which aspects of the solution structure are retained in the ion mobility measurement and which ones are not. Here, we apply our recently developed Structure Relaxation Approximation (SRA) method in conjunction with trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) to probe compaction of the human protein chemokine (C-C motif) ligand 5 (also CCL5). Ion mobility spectra are recorded for various charge states and solution conditions of CCL5 under both “soft” and collisionally-activated conditions. Our data show that the SRA reproduces the overall trends in the experimental spectra: (1) the compaction of the CCL5 structure as seen in the experiments; (2) the general increase in the cross section for the various charge states; and (3) the increase in cross section after collisional-activation. The SRA attributes the compaction of the CCL5 structure mainly to the folding of the unstructured N-terminus onto the central Greek key motif of CCL5. By contrast, the SRA indicates that native residue-residue contacts present in the NMR structure are largely retained. Additionally, our analysis indicates that accurate treatment of proton transfer processes during the structural relaxation process would significantly improve the structural interpretation of ion mobility data by the SRA.
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•Trapped Ion Mobility Spectrometry (TIMS) analysis of protein chemokine (C-C motif) ligand 5 (CCL5).•Structural interpretation of TIMS spectra with Structure Relaxation Approximation (SRA).•SRA reproduces the overall trends in the TIMS spectra recorded at various conditions for CCL5.•SRA suggests that the native contacts of CCL5 are largely retained.
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► We develop the projected superposition approximation (PSA) to compute molecular collision cross sections measured in ion-mobility experiments. ► Molecular collision cross sections ...are computed as a projection approximation modified to account for collective size and shape effects. ► We show that the PSA algorithm is able to handle the geometries typical to proteins while being computationally highly efficient.
A projected superposition approximation (PSA) to compute molecular collision cross sections measured in ion-mobility experiments is developed. In the framework of the PSA, molecular collision cross sections are computed as a projection approximation modified to account for collective size and shape effects. Illustrative calculations on a range of molecular structures demonstrate that the PSA algorithm is able to handle the complex molecular shapes (concave, convex, pores, cavities, channels) as well as the range in molecular size typical to proteins. Our results indicate strong numerical agreement with the accurate trajectory method while only a small fraction of the computational demand is required.
The local collision probability approximation (LCPA) method is introduced to compute molecular momentum transfer cross sections for comparison to ion mobility experiments. The LCPA replaces the ...(non-local) scattering trajectory used in the trajectory method to describe the collision process by a (local) collision probability function. This momentum transfer probability is computed using the exact same analyte-buffer interaction potential as used in the trajectory method. Subsequently, the momentum transfer cross section
Ω
LCPA
(
T
) is calculated in a projection-type manner (corrected for shape effects through a shape factor). Benchmark calculations on a set of 208 carbon clusters with a range of molecular size and degree of concavity demonstrate that LCPA and trajectory calculations agree closely with one another. The results discussed here indicate that the LCPA is suitable to efficiently calculate momentum transfer cross sections for use in ion mobility spectrometry in conjunction with different buffer gases.
The local collision probability approximation (LCPA) method is introduced to compute molecular momentum transfer cross sections for comparison to ion mobility experiments.
Carbohydrates play important roles in biological processes, but their identification remains a significant analytical problem. While mass spectrometry has increasingly enabled the elucidation of ...carbohydrates, current approaches are limited in their abilities to differentiate isomeric carbohydrates when these are not separated prior to tandem–mass spectrometry analysis. This analytical challenge takes on increased relevance because of the pervasive presence of isomeric carbohydrates in biological systems. Here, we demonstrate that TIMS2–MS2 workflows enabled by tandem-trapped ion mobility spectrometry–mass spectrometry (tTIMS/MS) provide a general approach to differentiate isomeric, nonseparated carbohydrates. Our analysis shows that (1) cross sections measured by TIMS are sufficiently precise and robust for ion identification; (2) fragment ion cross sections from TIMS2 analysis can be analytically exploited to identify carbohydrate precursors even if the precursor ions are not separated by TIMS; (3) low-abundant fragment ions can be exploited to identify carbohydrate precursors even if the precursor ions are not separated by IMS. (4) MS2 analysis of fragment ions produced by TIMS2 can be used to validate and/or further characterize carbohydrate structures. Taken together, our analysis underlines the opportunities that tandem-ion mobility spectrometry/MS methods offer for the characterization of mixtures of isomeric carbohydrates.
This review considers noncovalent bonds between divalent chalcogen centers. In the first part we present X-ray data taken from the solid state structures of dimethyl- and diphenyl-dichalcogenides as ...well as oligoalkynes kept by alkyl-sulfur, -selenium, and -tellurium groups. Furthermore, we analyzed the solid state structures of medium sized (12–24 ring size) selenium coronands and medium to large rings with alkyne and alkene units between two chalcogen centers. The crystal structures of the cyclic structures revealed columnar stacks with close contacts between neighboring rings via noncovalent interactions between the chalcogen centers. To get larger space within the cavities, rings with diyne units between the chalcogen centers were used. These molecules showed channel-like structures in the solid state. The flexibility of the rings permits inclusion of guest molecules such as five-membered heterocycles and aromatic six-membered rings. In the second part we discuss the results of quantum chemical calculations. To treat properly the noncovalent bonding between chalcogens, we use diffuse augmented split valence basis sets in combination with electron correlation methods. Our model substances were 16 dimers consisting of two Me-X-Me (X = O, S, Se, Te) pairs and dimers of Me-X-Me/Me-X-CN (X = O, S, Se, Te) pairs. The calculations show the anticipated increase of the interaction energy from (Me-O-Me)2 (−2.15 kcal/mol) to (Me-O-Me/Me-Te-CN) (−6.59 kcal/mol). An analysis by the NBO method reveals that in the case of the chalcogen centers O and S the hydrogen bridges between the molecules dominate. However, in the case of Se and Te the major bonding between the pairs originates from dispersion forces between the chalcogen centers. It varies between −1.7 and −4.0 kcal/mol.
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