Biological signalling activity measurements using mass spectrometry

2011 ◽  
Vol 434 (2) ◽  
pp. 189-199 ◽  
Author(s):  
Pedro R. Cutillas ◽  
Claus Jørgensen
Keyword(s):  
Mass Spectrometry ◽  
Present Review ◽  
System Level ◽  
Comprehensive Understanding ◽  
Disease Biology ◽  
Activity Measurements

MS (mass spectrometry) techniques are rapidly evolving to high levels of performance and robustness. This is allowing the application of these methods to the interrogation of signalling networks with unprecedented depth and accuracy. In the present review we discuss how MS-based multiplex quantification of kinase activities and phosphoproteomics provide complementary means to assess biological signalling activity. In addition, we discuss how a wider application of these analytical concepts to quantify kinase signalling will result in a more comprehensive understanding of normal and disease biology at the system level.

Add salt, add sugar: N-glycosylation in Haloferax volcanii

2013 ◽  
Vol 41 (1) ◽  
pp. 432-435 ◽  
Author(s):  
Lina Kaminski ◽  
Shai Naparstek ◽  
Lina Kandiba ◽  
Chen Cohen-Rosenzweig ◽  
Adi Arbiv ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Biology ◽  
Haloferax Volcanii ◽  
Present Review ◽  
Post Translational Modification ◽  
Environmental Salinity ◽  
Native Proteins ◽  
Domains Of Life ◽  
Adaptive Role

Although performed by members of all three domains of life, the archaeal version of N-glycosylation remains the least understood. Studies on Haloferax volcanii have, however, begun to correct this situation. A combination of bioinformatics, molecular biology, biochemical and mass spectrometry approaches have served to delineate the Agl pathway responsible for N-glycosylation of the S-layer glycoprotein, a reporter of this post-translational modification in Hfx. volcanii. More recently, differential N-glycosylation of the S-layer glycoprotein as a function of environmental salinity was demonstrated, showing that this post-translational modification serves an adaptive role in Hfx. volcanii. Furthermore, manipulation of the Agl pathway, together with the capability of Hfx. volcanii to N-glycosylate non-native proteins, forms the basis for establishing this species as a glyco-engineering platform. In the present review, these and other recent findings are addressed.

An Investigation Into Modeling and Solution Strategies for Optimal Design and Control

2000 ◽  
Author(s):  
Julie A. Reyer ◽  
Panos Y. Papalambros
Keyword(s):  
System Level ◽  
Simple Problem ◽  
Concurrent Design ◽  
Comprehensive Understanding ◽  
Solution Strategies ◽  
Advantages And Disadvantages ◽  
Embodiment Design ◽  
And Control ◽  
Monotonicity Analysis

Abstract Combined optimal embodiment design and control is increasingly necessary in designing modern artifacts. Several strategies for achieving such a system-level optimum were examined previously in the context of a case study. Since different strategies often lead to different results, a more comprehensive understanding of the relative advantages and disadvantages of these “concurrent design” processes is desirable. The present article explores this question using a very simple problem to demonstrate the complexities involved. Monotonicity analysis and a decomposition framework help explain the reasons for arriving at different results, even unexpectedly. Conclusions are drawn regarding the effectiveness of the various modeling formulations.

scholarly journals Proteomics: a powerful tool to study plant responses to biotic stress

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Yahui Liu ◽  
Song Lu ◽  
Kefu Liu ◽  
Sheng Wang ◽  
Luqi Huang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biotic Stress ◽  
Resistance Mechanisms ◽  
Current Status ◽  
Biological Research ◽  
Plant Responses ◽  
Biological Functions ◽  
Comprehensive Understanding ◽  
Post Translational Modifications ◽  
Research Challenges

AbstractIn recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.

scholarly journals Electrospray and tandem mass spectrometry in biochemistry

2001 ◽  
Vol 355 (3) ◽  
pp. 545-561 ◽  
Author(s):  
William J. GRIFFITHS ◽  
Andreas P. JONSSON ◽  
Suya LIU ◽  
Dilip K. RAI ◽  
Yuqin WANG
Keyword(s):  
Mass Spectrometry ◽  
Present Review ◽  
Tandem Ms ◽  
Tandem Mass ◽  
Mass Analysis ◽  
Soft Ionization ◽  
Excellent Work ◽  
Ionization Mode ◽  
Design And Manufacture ◽  
Ionization Methods

Over the last 20 years, biological MS has changed out of all recognition. This is primarily due to the development in the 1980s of ‘soft ionization’ methods that permit the ionization and vaporization of large, polar, and thermally labile biomolecules. These developments in ionization mode have driven the design and manufacture of smaller and cheaper mass analysers, making the mass spectrometer a routine instrument in the biochemistry laboratory today. In the present review the revolutionary ‘soft ionization’ methods will be discussed with particular reference to electrospray. The mass analysis of ions will be described, and the concept of tandem MS introduced. Where appropriate, examples of the application of MS in biochemistry will be provided. Although the present review will concentrate on the MS of peptides/proteins and lipids, all classes of biomolecules can be analysed, and much excellent work has been done in the fields of carbohydrate and nucleic acid biochemistry.

scholarly journals Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Martin Steger ◽  
Vadim Demichev ◽  
Mattias Backman ◽  
Uli Ohmayer ◽  
Phillip Ihmor ◽  
...  
Keyword(s):  
Neural Network ◽  
Mass Spectrometry ◽  
Sample Preparation ◽  
Mode Of Action ◽  
System Level ◽  
High Temporal Resolution ◽  
Time Resolved ◽  
Data Independent Acquisition ◽  
Wide Scale

AbstractMass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA)-MS and neural network-based data processing specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples identification numbers to 70,000 ubiquitinated peptides in single MS runs, while significantly improving robustness and quantification precision. Upon inhibition of the oncology target USP7, we simultaneously record ubiquitination and consequent changes in abundance of more than 8,000 proteins at high temporal resolution. While ubiquitination of hundreds of proteins increases within minutes of USP7 inhibition, we find that only a small fraction of those are ever degraded, thereby dissecting the scope of USP7 action. Our method enables rapid mode-of-action profiling of candidate drugs targeting DUBs or ubiquitin ligases at high precision and throughput.

scholarly journals A Glimpse to Background and Characteristics of Major Molecular Biological Networks

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Md. Altaf-Ul-Amin ◽  
Tetsuo Katsuragi ◽  
Tetsuo Sato ◽  
Shigehiko Kanaya
Keyword(s):  
High Throughput ◽  
Biological Networks ◽  
System Level ◽  
Data Sets ◽  
Topological Properties ◽  
Comprehensive Understanding ◽  
Data Intensive ◽  
Huge Data ◽  
Mutual Relations ◽  
Level Analysis

Recently, biology has become a data intensive science because of huge data sets produced by high throughput molecular biological experiments in diverse areas including the fields of genomics, transcriptomics, proteomics, and metabolomics. These huge datasets have paved the way for system-level analysis of the processes and subprocesses of the cell. For system-level understanding, initially the elements of a system are connected based on their mutual relations and a network is formed. Among omics researchers, construction and analysis of biological networks have become highly popular. In this review, we briefly discuss both the biological background and topological properties of major types of omics networks to facilitate a comprehensive understanding and to conceptualize the foundation of network biology.

scholarly journals Absolute and relative measurement of the 243Am half-life

2020 ◽  
Vol 326 (3) ◽  
pp. 1785-1793 ◽  
Author(s):  
M. Marouli ◽  
S. Pommé ◽  
V. Jobbágy ◽  
H. Stroh ◽  
R. Van Ammel ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Alpha Particle ◽  
Half Life ◽  
Specific Activity ◽  
Isotope Dilution Mass Spectrometry ◽  
Standard Uncertainty ◽  
Mass Content ◽  
A Value ◽  
Activity Measurements ◽  
Relative Standard

AbstractThe half-life of 243Am has been measured by an absolute and a relative method, i.e. by determining the specific activity of 243Am and the specific activity ratio with 241Am. A mixed 241,243Am reference material was produced and certified for its americium mass content and its isotope amount ratios. The characterisation of the mass content of 243Am was established by isotope dilution mass spectrometry using an 241Am spike, produced from highly enriched 241Pu material. The isotope amount ratios n(241Am)/n(243Am) and n(242mAm)/n(243Am) were measured by thermal ionisation mass spectrometry. Activity measurements were performed by alpha-particle counting at a defined solid angle, as well as high-resolution alpha-particle spectrometry. From the 243Am/241Am activity and isotopic amount ratios, a value of 16.988 (24) was derived for the 243Am/241Am half-life ratio. Using a value of 432.6 (6) a for the 241Am half-life, the corresponding 243Am half-life value, 7349 (15) a, is in good agreement with the result obtained from the absolute method, 7342 (14) a. The mean value, 7345 (14) a, agrees well with data from literature and lowers the relative standard uncertainty to 0.2%.

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