scholarly journals Monitoring the synthesis of biomolecules using mass spectrometry

2016 ◽  
Vol 374 (2079) ◽  
pp. 20150378 ◽  
Author(s):  
Masaru Miyagi ◽  
Takhar Kasumov
Keyword(s):  
Mass Spectrometry ◽  
Heavy Water ◽  
High Throughput ◽  
Biological Systems ◽  
Global Scale ◽  
Selective Synthesis ◽  
Quantitative Mass Spectrometry ◽  
Dynamic Nature ◽  
Diverse Range ◽  
Cellular Processes

The controlled and selective synthesis/clearance of biomolecules is critical for most cellular processes. In most high-throughput ‘omics’ studies, we measure the static quantities of only one class of biomolecules (e.g. DNA, mRNA, proteins or metabolites). It is, however, important to recognize that biological systems are highly dynamic in which biomolecules are continuously renewed and different classes of biomolecules interact and affect each other's production/clearance. Therefore, it is necessary to measure the turnover of diverse classes of biomolecules to understand the dynamic nature of biological systems. Herein, we explain why the kinetic analysis of a diverse range of biomolecules is important and how such an analysis can be done. We argue that heavy water ( 2 H 2 O) could be a universal tracer for monitoring the synthesis of biomolecules on a global scale. This article is part of the themed issue ‘Quantitative mass spectrometry’.

scholarly journals Quantitative Mass Spectrometry for Bacterial Protein Toxins — A Sensitive, Specific, High-Throughput Tool for Detection and Diagnosis

Molecules ◽  
2011 ◽  
Vol 16 (3) ◽  
pp. 2391-2413 ◽  
Author(s):  
Anne E. Boyer ◽  
Maribel Gallegos-Candela ◽  
Renato C. Lins ◽  
Zsuzsanna Kuklenyik ◽  
Adrian Woolfitt ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Bacterial Protein ◽  
Quantitative Mass Spectrometry ◽  
Protein Toxins ◽  
Detection And Diagnosis

scholarly journals Keeping track of time: The fundamentals of cellular clocks

2020 ◽  
Vol 219 (11) ◽  
Author(s):  
Colin R. Gliech ◽  
Andrew J. Holland
Keyword(s):  
Biological Systems ◽  
Design Principles ◽  
Special Consideration ◽  
Intercellular Signaling ◽  
Biochemical Reactions ◽  
Diverse Range ◽  
Cellular Processes ◽  
The Common ◽  
Biochemical Components ◽  
Time Frames

Biological timekeeping enables the coordination and execution of complex cellular processes such as developmental programs, day/night organismal changes, intercellular signaling, and proliferative safeguards. While these systems are often considered separately owing to a wide variety of mechanisms, time frames, and outputs, all clocks are built by calibrating or delaying the rate of biochemical reactions and processes. In this review, we explore the common themes and core design principles of cellular clocks, giving special consideration to the challenges associated with building timers from biochemical components. We also outline how evolution has coopted time to increase the reliability of a diverse range of biological systems.

scholarly journals High-throughput quantitative top-down proteomics

2020 ◽  
Vol 16 (2) ◽  
pp. 91-99 ◽  
Author(s):  
Kellye A. Cupp-Sutton ◽  
Si Wu
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Quantitative Methods ◽  
Biological Systems ◽  
Top Down ◽  
P Application ◽  
Top Down Mass Spectrometry

Application of quantitative methods to top-down mass spectrometry has illustrated the importance of proteoforms and proteoform abundance in biological systems.

scholarly journals Towards quantitative mass spectrometry-based metabolomics in microbial and mammalian systems

2016 ◽  
Vol 374 (2079) ◽  
pp. 20150363 ◽  
Author(s):  
Rahul Vijay Kapoore ◽  
Seetharaman Vaidyanathan
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Biological Systems ◽  
High Sensitivity ◽  
Quantitative Mass Spectrometry ◽  
Small Molecular Weight ◽  
Quantitative Changes ◽  
Analytical Approaches

Metabolome analyses are a suite of analytical approaches that enable us to capture changes in the metabolome (small molecular weight components, typically less than 1500 Da) in biological systems. Mass spectrometry (MS) has been widely used for this purpose. The key challenge here is to be able to capture changes in a reproducible and reliant manner that is representative of the events that take place in vivo . Typically, the analysis is carried out in vitro , by isolating the system and extracting the metabolome. MS-based approaches enable us to capture metabolomic changes with high sensitivity and resolution. When developing the technique for different biological systems, there are similarities in challenges and differences that are specific to the system under investigation. Here, we review some of the challenges in capturing quantitative changes in the metabolome with MS based approaches, primarily in microbial and mammalian systems. This article is part of the themed issue ‘Quantitative mass spectrometry’.

scholarly journals Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism

2016 ◽  
Vol 88 (22) ◽  
pp. 11139-11146 ◽  
Author(s):  
Jeniffer V. Quijada ◽  
Nicholas D. Schmitt ◽  
Joseph P. Salisbury ◽  
Jared R. Auclair ◽  
Jeffrey N. Agar
Keyword(s):  
Mass Spectrometry ◽  
Heavy Water ◽  
Intact Protein ◽  
Quantitative Mass Spectrometry ◽  
Protein Mass

Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

2008 ◽  
Vol 86 (2) ◽  
pp. 137-148 ◽  
Author(s):  
Jeffrey C. Smith ◽  
Daniel Figeys
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Review Process ◽  
Peer Review Process ◽  
Cellular Systems ◽  
Post Translational Modification ◽  
Dynamic Nature ◽  
Cellular Processes ◽  
Recent Developments ◽  
Selection Of

Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.

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