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Mass Spectrometry Reviews

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https://www.readbyqxmd.com/read/29130504/mass-spectrometry-based-metabolomics-targeting-the-crosstalk-between-gut-microbiota-and-brain-in-neurodegenerative-disorders
#1
REVIEW
Hemi Luan, Xian Wang, Zongwei Cai
Metabolomics seeks to take a "snapshot" in a time of the levels, activities, regulation and interactions of all small molecule metabolites in response to a biological system with genetic or environmental changes. The emerging development in mass spectrometry technologies has shown promise in the discovery and quantitation of neuroactive small molecule metabolites associated with gut microbiota and brain. Significant progress has been made recently in the characterization of intermediate role of small molecule metabolites linked to neural development and neurodegenerative disorder, showing its potential in understanding the crosstalk between gut microbiota and the host brain...
November 12, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/29120505/a-tutorial-in-small-molecule-identification-via-electrospray-ionization-mass-spectrometry-the-practical-art-of-structural-elucidation
#2
REVIEW
Thomas De Vijlder, Dirk Valkenborg, Filip Lemière, Edwin P Romijn, Kris Laukens, Filip Cuyckens
The identification of unknown molecules has been one of the cornerstone applications of mass spectrometry for decades. This tutorial reviews the basics of the interpretation of electrospray ionization-based MS and MS/MS spectra in order to identify small-molecule analytes (typically below 2000 Da). Most of what is discussed in this tutorial also applies to other atmospheric pressure ionization methods like atmospheric pressure chemical/photoionization. We focus primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds, rather than describing strategies for large-scale identification in complex samples...
November 9, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/29120501/analysis-of-the-plasma-proteome-using-itraq-and-tmt-based-isobaric-labeling
#3
REVIEW
Robert Moulder, Santosh D Bhosale, David R Goodlett, Riitta Lahesmaa
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches...
November 9, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/29084367/ion-traps-in-modern-mass-spectrometry
#4
REVIEW
Dirk Nolting, Robert Malek, Alexander Makarov
This review is devoted to trapping mass spectrometry wherein ions are confined by electromagnetic fields for prolonged periods of time within limited volume, with mass measurement taking place within the same volume. Three major types of trapping mass spectrometers are discussed, specifically radiofrequency ion trap, Fourier transform ion cyclotron resonance and Orbitrap. While these three branches are intricately interwoven with each other over their recent history, they also differ greatly in their fundamentals, roots and historical origin...
October 30, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/29073341/metabolomics-toward-personalized-medicine
#5
REVIEW
Minnie Jacob, Andreas L Lopata, Majed Dasouki, Anas M Abdel Rahman
Metabolomics, which is the metabolites profiling in biological matrices, is a key tool for biomarker discovery and personalized medicine and has great potential to elucidate the ultimate product of the genomic processes. Over the last decade, metabolomics studies have identified several relevant biomarkers involved in complex clinical phenotypes using diverse biological systems. Most diseases result in signature metabolic profiles that reflect the sums of external and internal cellular activities. Metabolomics has a major role in clinical practice as it represents >95% of the workload in clinical laboratories worldwide...
October 26, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/29029360/laser-desorption-ionization-mass-spectrometry-recent-progress-in-matrix-free-and-label-assisted-techniques
#6
REVIEW
Arundhoti Mandal, Monisha Singha, Partha Sarathi Addy, Amit Basak
The MALDI-based mass spectrometry, over the last three decades, has become an important analytical tool. It is a gentle ionization technique, usually applicable to detect and characterize analytes with high molecular weights like proteins and other macromolecules. The earlier difficulty of detection of analytes with low molecular weights like small organic molecules and metal ion complexes with this technique arose due to the cluster of peaks in the low molecular weight region generated from the matrix. To detect such molecules and metal ion complexes, a four-prong strategy has been developed...
October 13, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28902424/anatomy-and-evolution-of-database-search-engines-a-central-component-of-mass-spectrometry-based-proteomic-workflows
#7
REVIEW
Kenneth Verheggen, Helge Raeder, Frode S Berven, Lennart Martens, Harald Barsnes, Marc Vaudel
Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher...
September 13, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27097288/qualitative-and-quantitative-characterization-of-protein-biotherapeutics-with-liquid-chromatography-mass-spectrometry
#8
REVIEW
Miao Qu, Bo An, Shichen Shen, Ming Zhang, Xiaomeng Shen, Xiaotao Duan, Joseph P Balthasar, Jun Qu
In the last decade, the advancement of liquid chromatography mass spectrometry (LC/MS) techniques has enabled their broad application in protein characterization, both quantitatively and qualitatively. Owing to certain important merits of LC/MS techniques (e.g., high selectivity, flexibility, and rapid method development), LC/MS assays are often deemed as preferable alternatives to conventional methods (e.g., ligand-binding assays) for the analysis of protein biotherapeutics. At the discovery and development stages, LC/MS is generally employed for two purposes absolute quantification of protein biotherapeutics in biological samples and qualitative characterization of proteins...
November 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26873676/single-molecule-mass-spectrometry
#9
REVIEW
David Z Keifer, Martin F Jarrold
In single-molecule mass spectrometry, the mass of each ion is measured individually; making it suitable for the analysis of very large, heterogeneous objects that cannot be analyzed by conventional means. A range of single-molecule mass spectrometry techniques has been developed, including time-of-flight with cryogenic detectors, a quadrupole ion trap with optical detection, single-molecule Fourier transform ion cyclotron resonance, charge detection mass spectrometry, quadrupole ion traps coupled to charge detector plates, and nanomechanical oscillators...
November 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26773411/selection-of-internal-standards-for-accurate-quantification-of-complex-lipid-species-in-biological-extracts-by-electrospray-ionization-mass-spectrometry-what-how-and-why
#10
REVIEW
Miao Wang, Chunyan Wang, Xianlin Han
Lipidomics is rapidly expanding because of the great facilitation of recent advances in, and novel applications of, electrospray ionization mass spectrometry techniques. The greatest demands have been for successful quantification of lipid classes, subclasses, and individual molecular species in biological samples at acceptable accuracy. This review addresses the selection of internal standards in different methods for accurate quantification of individual lipid species. The principles of quantification with electrospray ionization mass spectrometry are first discussed to recognize the essentials for quantification...
November 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26763661/recent-advances-in-mass-spectrometric-analysis-of-protein-deamidation
#11
REVIEW
Piliang Hao, Sunil S Adav, Xavier Gallart-Palau, Siu Kwan Sze
Protein deamidation has been proposed to represent a "molecular clock" that progressively disrupts protein structure and function in human degenerative diseases and natural aging. Importantly, this spontaneous process can also modify therapeutic proteins by altering their purity, stability, bioactivity, and antigenicity during drug synthesis and storage. Deamidation occurs non-enzymatically in vivo, but can also take place spontaneously in vitro, hence artificial deamidation during proteomic sample preparation can hamper efforts to identify and quantify endogenous deamidation of complex proteomes...
November 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28453879/computers-in-mass-spectrometry
#12
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27741559/the-arc-of-mass-spectrometry-exchange-formats-is-long-but-it-bends-toward-hdf5
#13
REVIEW
Manor Askenazi, Hisham Ben Hamidane, Johannes Graumann
The evolution of data exchange in Mass Spectrometry spans decades and has ranged from human-readable text files representing individual scans or collections thereof (McDonald et al., 2004) through the official standard XML-based (Harold, Means, & Udemadu, 2005) data interchange standard (Deutsch, 2012), to increasingly compressed (Teleman et al., 2014) variants of this standard sometimes requiring purely binary adjunct files (Römpp et al., 2011). While the desire to maintain even partial human readability is understandable, the inherent mismatch between XML's textual and irregular format relative to the numeric and highly regular nature of actual spectral data, along with the explosive growth in dataset scales and the resulting need for efficient (binary and indexed) access has led to a phenomenon referred to as "technical drift" (Davis, 2013)...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27602546/computational-methods-and-challenges-in-hydrogen-deuterium-exchange-mass-spectrometry
#14
REVIEW
Jürgen Claesen, Tomasz Burzykowski
Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27403644/tandem-mass-spectral-libraries-of-peptides-and-their-roles-in-proteomics-research
#15
REVIEW
Wenguang Shao, Henry Lam
Proteomics is a rapidly maturing field aimed at the high-throughput identification and quantification of all proteins in a biological system. The cornerstone of proteomic technology is tandem mass spectrometry of peptides resulting from the digestion of protein mixtures. The fragmentation pattern of each peptide ion is captured in its tandem mass spectrum, which enables its identification and acts as a fingerprint for the peptide. Spectral libraries are simply searchable collections of these fingerprints, which have taken on an increasingly prominent role in proteomic data analysis...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26799864/peptide-retention-time-prediction
#16
REVIEW
Luminita Moruz, Lukas Käll
Most methods for interpreting data from shotgun proteomics experiments are to large degree dependent on being able to predict properties of peptide-ions. Often such predicted properties are limited to molecular mass and fragment spectra, but here we put focus on a perhaps underutilized property, a peptide's chromatographic retention time. We review a couple of different principles of retention time prediction,and their applications within computational proteomics. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:615-623, 2017...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26763615/mining-molecular-structure-databases-identification-of-small-molecules-based-on-fragmentation-mass-spectrometry-data
#17
REVIEW
Franziska Hufsky, Sebastian Böcker
Mass spectrometry (MS) is a key technology for the analysis of small molecules. For the identification and structural elucidation of novel molecules, new approaches beyond straightforward spectral comparison are required. In this review, we will cover computational methods that help with the identification of small molecules by analyzing fragmentation MS data. We focus on the four main approaches to mine a database of metabolite structures, that is rule-based fragmentation spectrum prediction, combinatorial fragmentation, competitive fragmentation modeling, and molecular fingerprint prediction...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26709718/protein-complex-analysis-from-raw-protein-lists-to-protein-interaction-networks
#18
REVIEW
Pieter Meysman, Kevin Titeca, Sven Eyckerman, Jan Tavernier, Bart Goethals, Lennart Martens, Dirk Valkenborg, Kris Laukens
The elucidation of molecular interaction networks is one of the pivotal challenges in the study of biology. Affinity purification-mass spectrometry and other co-complex methods have become widely employed experimental techniques to identify protein complexes. These techniques typically suffer from a high number of false negatives and false positive contaminants due to technical shortcomings and purification biases. To support a diverse range of experimental designs and approaches, a large number of computational methods have been proposed to filter, infer and validate protein interaction networks from experimental pull-down MS data...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26670565/proteogenomics-from-a-bioinformatics-angle-a-growing-field
#19
REVIEW
Gerben Menschaert, David Fenyö
Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies. Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments...
September 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28802010/quality-control-in-mass-spectrometry-based-proteomics
#20
REVIEW
Wout Bittremieux, David L Tabb, Francis Impens, An Staes, Evy Timmerman, Lennart Martens, Kris Laukens
Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results. A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages...
August 12, 2017: Mass Spectrometry Reviews
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