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Mass Spectrometry Reviews

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https://www.readbyqxmd.com/read/28902424/anatomy-and-evolution-of-database-search-engines-a-central-component-of-mass-spectrometry-based-proteomic-workflows
#1
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/28802010/quality-control-in-mass-spectrometry-based-proteomics
#2
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
https://www.readbyqxmd.com/read/28758227/standardization-approaches-in-absolute-quantitative-proteomics-with-mass-spectrometry
#3
REVIEW
Francisco Calderón-Celis, Jorge Ruiz Encinar, Alfredo Sanz-Medel
Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers...
July 31, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28691345/the-skyline-ecosystem-informatics-for-quantitative-mass-spectrometry-proteomics
#4
REVIEW
Lindsay K Pino, Brian C Searle, James G Bollinger, Brook Nunn, Brendan MacLean, Michael J MacCoss
Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.
July 9, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28453879/computers-in-mass-spectrometry
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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/28621908/correction
#13
(no author information available yet)
No abstract text is available yet for this article.
July 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27074547/application-of-mass-spectrometry-in-the-characterization-of-chemicals-in-coal-derived-liquids
#14
REVIEW
Fang-Jing Liu, Maohong Fan, Xian-Yong Wei, Zhi-Min Zong
Coal-derived liquids (CDLs) are primarily generated from pyrolysis, carbonization, gasification, direct liquefaction, low-temperature extraction, thermal dissolution, and mild oxidation. CDLs are important feedstocks for producing value-added chemicals and clean liquid fuels as well as high performance carbon materials. Accordingly, the compositional characterization of chemicals in CDLs at the molecular level with advanced analytical techniques is significant for the efficient utilization of CDLs. Although reviews on advancements have been rarely reported, great progress has been achieved in this area by using gas chromatography/mass spectrometry (GC/MS), two-dimensional GC-time of flight mass spectrometry (GC × GC-TOFMS), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)...
July 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26999732/the-allure-of-mass-spectrometry-from-an-earlyday-chemist-s-perspective
#15
REVIEW
László Tőkés
This reminiscing review article is an account of the author's fascination and involvements with mass spectrometry from the perspective of an organic chemist with an interest in natural product chemistry. It covers a period from 1961 through the mid 1990s as mass spectrometry evolved form a novelty technique to become a most widely used analytical technique. Following a brief synopsis of my pathway to mass spectrometry, my research efforts in this field are presented with a focus mainly on evolving principles and technologies which I had personal involvements with...
July 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26757103/a-review-on-the-determination-of-isotope-ratios-of-boron-with-mass-spectrometry
#16
REVIEW
Suresh Kumar Aggarwal, Chen-Feng You
The present review discusses different mass spectrometric techniques-viz, thermal ionization mass spectrometry (TIMS), inductively coupled plasma mass spectrometry (ICPMS), and secondary ion mass spectrometry (SIMS)-used to determine (11) B/(10) B isotope ratio, and concentration of boron required for various applications in earth sciences, marine geochemistry, nuclear technology, environmental, and agriculture sciences, etc. The details of the techniques-P-TIMS, which uses Cs2 BO2(+) , N-TIMS, which uses BO2(-) , and MC-ICPMS, which uses B(+) ions for bulk analysis or B(-) and B(+) ions for in situ micro-analysis with SIMS-are highlighted...
July 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/26728195/algorithms-and-design-strategies-towards-automated-glycoproteomics-analysis
#17
REVIEW
Han Hu, Kshitij Khatri, Joseph Zaia
Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data...
July 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28627748/on-line-reaction-monitoring-by-mass-spectrometry-modern-approaches-for-the-analysis-of-chemical-reactions
#18
REVIEW
Andrew Ray, Tony Bristow, Chris Whitmore, Jackie Mosely
The application of on-line mass spectrometry for direct analysis of chemical and other types of process continues to grow in importance and impact. The ability of the technique to characterize many aspects of a chemical reaction such as product and impurity formation, along with reactant consumption in a single experiment is key to its adoption and development. Innovations in ionization techniques and mass spectrometry instrumentation are enabling this adoption. An increasing range of ambient ionization techniques make on-line mass spectrometry applicable to a large range of chemistries...
June 19, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28621817/gas-phase-basicities-of-polyfunctional-molecules-part-6-cyanides-and-isocyanides
#19
REVIEW
Guy Bouchoux
This paper gathers structural and thermochemical informations related to the gas-phase basicity of molecules containing cyanides (nitriles) and isocyanides (isonitriles) functional groups. It constitutes the sixth part of a general review devoted to gas-phase basicities of polyfunctional compounds. A large corpus of cyanides and isocyanides molecules is examined under seven major chapters. In the first one, a rapid overview of the definitions and methods leading to gas-phase basicity, GB, proton affinity, PA, and protonation entropy, Δp S°, is given...
June 16, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28509357/characterization-of-microbial-mixtures-by-mass-spectrometry
#20
REVIEW
Todd R Sandrin, Plamen A Demirev
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike...
May 16, 2017: Mass Spectrometry Reviews
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