1,721,126 research outputs found
Differences in the Elemental Isotope Definition May Lead to Errors in Modern Mass-Spectrometry-Based Proteomics
No full textThe elemental isotope definition used to calculate the theoretical masses and isotope distribution of (bio)molecules is
considered to be a fixed, universal standard in mass-spectrometrybased proteomics. However, this is an incorrect assumption. In view of the ongoing advances in mass spectrometry technology, and in particular the ever-increasing mass precision, the elemental isotope definition and its variations should be taken into account. We illustrate the effect of the elemental isotope uncertainty on the theoretical and experimental masses with theoretical calculations and examples.The authors are grateful to the editor and the reviewers for their insightful comments. All of these comments were most helpful and have resulted in an improved text. The authors would like to acknowledge IUPAC and M. Wieser for granting us permission to use Figure 3. D.V. acknowledges support from the SBO grant "InSPECtor" (120025) of the Flemish agency for Innovation by Science and Technology (ENT). F.L. acknowledges support from the Research Foundation - Flanders (FWO)
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Computational Tools for Hydrogen–Deuterium Exchange Mass Spectrometry Data Analysis
Full text linkHydrogen-deuterium exchange (HDX) has become a pivotal method for investigating the structural and dynamic properties of proteins. The versatility and sensitivity of mass spectrometry (MS) made the technique the ideal companion for HDX, and today HDX-MS is addressing a growing number of applications in both academic research and industrial settings. The prolific generation of experimental data has spurred the concurrent development of numerous computational tools, designed to automate parts of the workflow while employing different strategies to achieve common objectives. Various computational methods are available to perform automated peptide searches and identification; different statistical tests have been implemented to quantify differences in the exchange pattern between two or more experimental conditions; alternative strategies have been developed to deconvolve and analyze peptides showing multimodal behavior; and different algorithms have been proposed to computationally increase the resolution of HDX-MS data, with the ultimate aim to provide information at the level of the single residue. This review delves into a comprehensive examination of the merits and drawbacks associated with the diverse strategies implemented by software tools for the analysis of HDX-MS data
Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry
No full textElectron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact. The obtained fragmentation spectra provide valuable information for sequence and structure analyses. In this study, we propose a formal mathematical model of the ETD fragmentation process in the form of a system of stochastic differential equations describing its joint dynamics. Parameters of the model correspond to the rates of occurring reactions. Their estimates for various experimental settings give insight into the dynamics of the ETD process. We estimate the model parameters from the relative quantities of fragmentation products in a given mass spectrum by solving a nonlinear optimization problem. The cost function penalizes for the differences between the analytically derived average number of reaction products and their experimental counterparts. The presented method proves highly robust to noise in silico. Moreover, the model can explain a considerable amount of experimental results for a wide range of instrumentation settings. The implementation of the presented workflow, code-named ETDetective, is freely available under the two-clause BSD license.This work was partially supported by the National Science Centre grant numbers 2013/09/B/ST6/01575, 2014/12/W/ST5/00592, and 2015/17/N/ST6/03565 and the SBO grant InSPECtor (120025) of the Flemish Agency for Innovation by Science and Technology (IWT). The authors thank the Research Foundation-Flanders (FWO) for funding a PhD fellowship (F.L.). The Synapt G2 mass spectrometer is funded by a grant from the Hercules Foundation-Flanders
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Novel native mass spectrometry and ion mobility approaches for the characterization of membrane proteins and pores
No full textAbstract: Native mass spectrometry has shown over the past years to be a very useful tool in the investigation of membrane proteins and pores, which provides additional information next to the conventional structural techniques. This information concerns for example the stoichiometry of complexes and structural information. In recent years native mass spectrometry has shown to be very useful for the investigation of large noncovalent, mainly globular structures. In this thesis different projects are presented and discussed showing the versatility of native mass spectrometry; including membrane associated proteins and nanopores build from custom designed DNA strands. To investigate each of the different projects ion mobility and mass spectrometric techniques were used. This also includes the methods of sample preparation required to transfer the samples into the gas phase without disturbing the complexes formed significantly. The BAX protein revealed to behave differently, when different detergents were present in solution above the critical micelle concentration or when binding the directly activating molecule BAM-7. Ion mobility and mass spectrometry show that it forms oligomers and conformational changes. Native mass spectrometry turned out to be very useful in the investigation of lipid interactions with membrane proteins. This was shown by MgtA membrane protein revealing a very specific binding of lipids. Native MS has shown to be very useful for observing of specifically bound lipids even when high concentrations of other lipid were present. DNA origami is a term used for artificial designed nano-structures from DNA building blocks. Within this thesis the formation of such a DNA nano-structure was investigated concerning the formation of a DNA nanopore. This pore is formed from different DNA strands which should only fit together in one possible manner. Using ion mobility mass spectrometry it was shown that the salt concentration, in the form of ammonium acetate, has a profound influence on the actual form of the hexameric pore
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry
No full textAbstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application
Mass spectrometry-based methods to explore higher-order protein structure : generating a fingerprint for biologics
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