scholarly journals Mass spectrometry as a quantitative tool in plant metabolomics

2016 ◽  
Vol 374 (2079) ◽  
pp. 20150370 ◽  
Author(s):  
Tiago F. Jorge ◽  
Ana T. Mata ◽  
Carla António
Keyword(s):  
Mass Spectrometry ◽  
Chemical Species ◽  
Chemical Properties ◽  
Research Field ◽  
Plant Metabolomics ◽  
Wide Range ◽  
Metabolite Pool ◽  
Development And Validation ◽  
Analytical Tools ◽  
Quantitative Tool

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided. This article is part of the themed issue ‘Quantitative mass spectrometry’.

212 Fatty Acid Analysis and Composition in Meat by Mass Spectrometry

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 111-112
Author(s):  
Thu Dinh
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acids ◽  
Fatty Acid ◽  
Methyl Esters ◽  
Meat Products ◽  
Chemical Properties ◽  
Fatty Acid Analysis ◽  
Animal Fats ◽  
Wide Range ◽  
Mass Spectrometry Technology

Abstract Fatty acids determine the physical and chemical properties of fats. Animal fats, regardless of species, have more saturated and monounsaturated than polyunsaturated fatty acids. The major fatty acids in meat are palmitic (16:0), stearic (18:0), palmitoleic (16:1), oleic (18:1), linoleic (18:2), and linolenic (18:3) acids, among which oleic acid is the most predominant. Arachidonic acid (20:4 cis 5,8,11,14) is an essential fatty acid only found in animal fats and can be used as a quality control indicator in the fatty acid analysis. Fatty acid analysis has been traditionally performed by gas chromatography (GC) of volatile fatty acid derivatives, prominently the methyl esters, and flame ionization detection (FID), in which the carbon chain of fatty acids is degraded to the formylium ion CHO+. The FID is very sensitive and is the most widely used detection method for GC, providing a linear response, i.e., peak area, over a wide range of concentrations. Researchers have been used the FID peak area to calculate the percentages of fatty acids. However, the FID is a “carbon counter” and relies on the “equal per carbon” rule; therefore, at the same molar concentration, fatty acids with a different number of carbons produce different peak areas. The recent development of mass spectrometry technology has improved the specificity of fatty acid detection. Specific target and qualifier ions provide better identification and more accurate quantification of fatty acid concentrations. Although fatty acids can be identified through comparing ion fragmentation with various databases, authentic standards are needed for quantification purposes. Using mass spectrometry, more than 50 fatty acids have been identified in meat samples. Some branched-chain fatty acids may have flavor, safety, and shelf life implications in meat products.

scholarly journals Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics

Molecules ◽  
2019 ◽  
Vol 24 (4) ◽  
pp. 701 ◽  
Author(s):  
Remigiusz Bąchor ◽  
Mateusz Waliczek ◽  
Piotr Stefanowicz ◽  
Zbigniew Szewczuk
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Chemical Properties ◽  
High Energy ◽  
Tandem Mass ◽  
Peptide Molecule ◽  
Wide Range ◽  
Potential Applications ◽  
Isobaric Tag ◽  
Modern Mass

Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups. They have the same molecular weights and chemical properties, but differ in the distribution of stable heavy isotopes. These tags are designed in such a way that during high energy collision induced dissociation (CID) by tandem mass spectrometry, the isobaric tag is fragmented in the specific linker region, yielding reporter ions with different masses. The mass shifts among the reporter groups are compensated by the balancing groups so that the overall mass is the same for all forms of the reagent. Samples of peptides are labeled with the isobaric mass tags in parallel and combined for analysis. Quantification of individual peptides is achieved by comparing the intensity of reporter ions in the tandem mass (MS/MS) spectra. Isobaric markers have found a wide range of potential applications in proteomics. However, the currently available isobaric labeling reagents have some drawbacks, such as high cost of production, insufficient selectivity of the derivatization, and relatively limited enhancement of sensitivity of the analysis. Therefore, efforts have been devoted to the development of new isobaric markers with increased usability. The search for new isobaric markers is focused on developing a more selective method of introducing a tag into a peptide molecule, increasing the multiplexicity of markers, lowering the cost of synthesis, and increasing the sensitivity of measurement by using ionization tags containing quaternary ammonium salts. Here, the trends in the design of new isobaric labeling reagents for quantitative proteomics isobaric derivatization strategies in proteomics are reviewed, with a particular emphasis on isobaric ionization tags. The presented review focused on different types of isobaric reagents used in quantitative proteomics, their chemistry, and advantages offer by their application.

scholarly journals Current analytical technologies and bioinformatic resources for plant metabolomics data

2021 ◽  
Author(s):  
Chigateri M. Vinay ◽  
Sanjay Kannath Udayamanoharan ◽  
Navya Prabhu Basrur ◽  
Bobby Paul ◽  
Padmalatha S. Rai
Keyword(s):  
Inorganic Compounds ◽  
Biological Data ◽  
Biological Information ◽  
Metabolomics Data ◽  
Primary And Secondary Metabolites ◽  
Chemical Structures ◽  
Plant Metabolomics ◽  
Wide Range ◽  
Analytical Tools

AbstractPlant metabolome as the downstream product in the biological information of flow starting from genomics is highly complex, and dynamically produces a wide range of primary and secondary metabolites, including ionic inorganic compounds, hydrophilic carbohydrates, amino acids, organic compounds, and compounds associated with hydrophobic lipids. The complex metabolites present in biological samples bring challenges to analytical tools for separating and characterization of the metabolites. Analytical tools such as nuclear magnetic resonance (NMR) and mass spectrometry have recently facilitated the separation, characterization, and quantification of diverse chemical structures. The massive amount of data generated from these analytical tools need to be handled using fast and accurate bioinformatics tools and databases. In this review, we focused on plant metabolomics data acquisition using various analytical tools and freely available workflows from raw data to meaningful biological data to help biologists and chemists to move at the same pace as computational biologists.

scholarly journals Plants Metabolome Study: Emerging Tools and Techniques

2021 ◽  
Author(s):  
Manish Kumar Patel ◽  
Sonika Pandey ◽  
Manoj Kumar ◽  
Intesaful Haque ◽  
Sikander Pal ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Breeding ◽  
Plant Biology ◽  
Gas Chromatography Mass Spectrometry ◽  
Ion Cyclotron Resonance ◽  
Laser Desorption Ionization ◽  
Metabolite Pool ◽  
Speed Up ◽  
Tools And Techniques ◽  
Analytical Tools

Metabolomics is now considered to be a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense response to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in molecular breeding and genome editing programs to develop superior next generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted method. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) and matrix-assisted laser desorption/ionization (MALDI) have speed up metabolic profiling in plants. Further, we deliver a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

scholarly journals Mass Spectrometry-Based Zebrafish Toxicometabolomics: A Review of Analytical and Data Quality Challenges

Metabolites ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 635
Author(s):  
Katyeny Manuela da Silva ◽  
Elias Iturrospe ◽  
Chloe Bars ◽  
Dries Knapen ◽  
Steven Van Cruchten ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Chemical Exposure ◽  
Research Field ◽  
In Vivo Studies ◽  
In Vitro Assays ◽  
Special Focus ◽  
Zebrafish Model ◽  
Wide Range

Metabolomics has achieved great progress over the last 20 years, and it is currently considered a mature research field. As a result, the number of applications in toxicology, biomarker, and drug discovery has also increased. Toxicometabolomics has emerged as a powerful strategy to provide complementary information to study molecular-level toxic effects, which can be combined with a wide range of toxicological assessments and models. The zebrafish model has gained importance in recent decades as a bridging tool between in vitro assays and mammalian in vivo studies in the field of toxicology. Furthermore, as this vertebrate model is a low-cost system and features highly conserved metabolic pathways found in humans and mammalian models, it is a promising tool for toxicometabolomics. This short review aims to introduce zebrafish researchers interested in understanding the effects of chemical exposure using metabolomics to the challenges and possibilities of the field, with a special focus on toxicometabolomics-based mass spectrometry. The overall goal is to provide insights into analytical strategies to generate and identify high-quality metabolomic experiments focusing on quality management systems (QMS) and the importance of data reporting and sharing.

scholarly journals Plants Metabolome Study: Emerging Tools and Techniques

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2409
Author(s):  
Manish Kumar Patel ◽  
Sonika Pandey ◽  
Manoj Kumar ◽  
Md Intesaful Haque ◽  
Sikander Pal ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
Defense Responses ◽  
Plant Biology ◽  
Gas Chromatography Mass Spectrometry ◽  
Ion Cyclotron Resonance ◽  
Metabolite Pool ◽  
Speed Up ◽  
Tools And Techniques ◽  
Analytical Tools

Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense responses to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted methods. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) matrix-assisted laser desorption/ionization (MALDI), ion mobility spectrometry (IMS) and nuclear magnetic resonance (NMR) have speed up precise metabolic profiling in plants. Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

Emerging Trends in Advanced Nanomaterials Based Electrochemical Genosensors

2019 ◽  
Vol 24 (31) ◽  
pp. 3697-3709 ◽  
Author(s):  
Mahima Kaushik ◽  
Sonia Khurana ◽  
Komal Mehra ◽  
Neelam Yadav ◽  
Sujeet Mishra ◽  
...  
Keyword(s):  
Direct Detection ◽  
High Surface ◽  
High Surface Area ◽  
Research Area ◽  
Nanostructured Material ◽  
Emerging Trends ◽  
Highly Sensitive ◽  
Wide Range ◽  
Development And Validation ◽  
Analytical Tools

Advanced nanomaterials indubitably represent one of the most propitious class of new materials due to their intriguing optical, electronic and redox properties. The incredible progress achieved in this research area has been propelled by the development of novel synthetic procedures owing to the emergence of nanotechnology and by the wide range of applications. These nanostructured materials possess high surface area, biocompatibility, nontoxicity and charge-sensitive conductance which have led to the development of simple, rapid, highly sensitive, inexpensive and portable electrochemical genosensors. This review accentuates on the development and validation of various advanced nanomaterials based electrochemical genosensors that utilize unique properties of nanomaterials for signal transduction purpose or as an electroactive species for direct detection of analyte. The intent is to highlight the recent progress on highly sensitive and flexible nanostructured material based electrochemical genosensors that have the potential to be developed as the next generation field-deployable analytical tools.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

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