scholarly journals A Multidimensional Mass Spectrometry-Based Workflow for De Novo Structural Elucidation of Oligosaccharides from Polysaccharides

2021 ◽  
Author(s):  
Juan Jose Castillo ◽  
Ace G. Galermo ◽  
Matthew J. Amicucci ◽  
Eshani Nandita ◽  
Garret Couture ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Structural Elucidation ◽  
Multidimensional Mass Spectrometry

Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry

2011 ◽  
Vol 37 (12) ◽  
pp. 1278-1288 ◽  
Author(s):  
Han-Chang SUN ◽  
Ji-Yang ZHANG ◽  
Hui LIU ◽  
Wei ZHANG ◽  
Chang-Ming XU ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
De Novo ◽  
Peptide Sequencing ◽  
Tandem Mass ◽  
Algorithm Development

Detection, Identification and Structural Elucidation of Flavonoids using Liquid Chromatography Coupled to Mass Spectrometry

2020 ◽  
Vol 24 (1) ◽  
pp. 104-112 ◽  
Author(s):  
Krzysztof Kamil Wojtanowski ◽  
Tomasz Mroczek
Keyword(s):  
Mass Spectrometry ◽  
Central Nervous System ◽  
Nuclear Magnetic Resonance ◽  
Liquid Chromatography ◽  
High Performance ◽  
Short Review ◽  
Structural Elucidation ◽  
High Throughput Analysis ◽  
Protective Actions ◽  
The Central Nervous System

Flavonoids are one of the most common secondary metabolites occurring in plants. Their activity in the Central Nervous System (CNS) including sedative, anxiolytic, anti-convulsive, anti-depressant and neuro-protective actions is well known and documented. The most popular methods for detection, identification and structural elucidation of flavonoids are these based on Nuclear Magnetic Resonance (NMR) and mass spectrometry (MS). NMR allows rapid, high throughput analysis of crude extracts and also gives stereochemical details about identified substances. However, these methods are expensive and less sensitive than MS-based techniques. Combining High Performance Liquid Chromatography (HPLC) with MS detection gives the most powerful tool for analysis of flavonoids occurring in plants. There is a lot of different approaches to use LC/MS based techniques for identification of flavonoids and this short review shows the most important.

Untangling the Metabolic Reprogramming in Brain Cancer: Discovering Key Molecular Players Using Mass Spectrometry

2019 ◽  
Vol 19 (17) ◽  
pp. 1521-1534 ◽  
Author(s):  
Anatoly Sorokin ◽  
Vsevolod Shurkhay ◽  
Stanislav Pekov ◽  
Evgeny Zhvansky ◽  
Daniil Ivanov ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Brain Cancer ◽  
De Novo ◽  
Aerobic Glycolysis ◽  
Lipid Production ◽  
Dietary Fatty Acids ◽  
Metabolic Reprogramming ◽  
Detection Methods ◽  
Malignant Cells ◽  
Proliferating Cells

Cells metabolism alteration is the new hallmark of cancer, as well as an important method for carcinogenesis investigation. It is well known that the malignant cells switch to aerobic glycolysis pathway occurring also in healthy proliferating cells. Recently, it was shown that in malignant cells de novo synthesis of the intracellular fatty acid replaces dietary fatty acids which change the lipid composition of cancer cells noticeably. These alterations in energy metabolism and structural lipid production explain the high proliferation rate of malignant tissues. However, metabolic reprogramming affects not only lipid metabolism but many of the metabolic pathways in the cell. 2-hydroxyglutarate was considered as cancer cell biomarker and its presence is associated with oxidative stress influencing the mitochondria functions. Among the variety of metabolite detection methods, mass spectrometry stands out as the most effective method for simultaneous identification and quantification of the metabolites. As the metabolic reprogramming is tightly connected with epigenetics and signaling modifications, the evaluation of metabolite alterations in cells is a promising approach to investigate the carcinogenesis which is necessary for improving current diagnostic capabilities and therapeutic capabilities. In this paper, we overview recent studies on metabolic alteration and oncometabolites, especially concerning brain cancer and mass spectrometry approaches which are now in use for the investigation of the metabolic pathway.

scholarly journals Identifying molecules as biosignatures with assembly theory and mass spectrometry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Stuart M. Marshall ◽  
Cole Mathis ◽  
Emma Carrick ◽  
Graham Keenan ◽  
Geoffrey J. T. Cooper ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Outer Space ◽  
Molecular Assembly ◽  
Detection Experiment ◽  
Complex Molecules ◽  
The World ◽  
Life Detection ◽  
Molecular Complexity ◽  
The Universe

AbstractThe search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry. This approach allows us to identify molecular biosignatures from a set of diverse samples from around the world, outer space, and the laboratory, demonstrating it is possible to build a life detection experiment based on MA that could be deployed to extraterrestrial locations, and used as a complexity scale to quantify constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital for finding life elsewhere in the universe or creating de-novo life in the lab.

ON PREPROCESSING AND ANTISYMMETRY IN DE NOVO PEPTIDE SEQUENCING: IMPROVING EFFICIENCY AND ACCURACY

2008 ◽  
Vol 06 (03) ◽  
pp. 467-492 ◽  
Author(s):  
KANG NING ◽  
NAN YE ◽  
HON WAI LEONG
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Computational Models ◽  
De Novo ◽  
Noise Removal ◽  
Peptide Sequencing ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

Peptide sequencing plays a fundamental role in proteomics. Tandem mass spectrometry, being sensitive and efficient, is one of the most commonly used techniques in peptide sequencing. Many computational models and algorithms have been developed for peptide sequencing using tandem mass spectrometry. In this paper, we investigate general issues in de novo sequencing, and present results that can be used to improve current de novo sequencing algorithms. We propose a general preprocessing scheme that performs binning, pseudo-peak introduction, and noise removal, and present theoretical and experimental analyses on each of the components. Then, we study the antisymmetry problem and current assumptions related to it, and propose a more realistic way to handle the antisymmetry problem based on analysis of some datasets. We integrate our findings on preprocessing and the antisymmetry problem with some current models for peptide sequencing. Experimental results show that our findings help to improve accuracies for de novo sequencing.

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