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

Protein mass measurement combined with mass spectrometric sequencing of protein digests for detection and characterization of protein modifications1

2006 ◽  
Vol 84 (7) ◽  
pp. 986-997 ◽  
Author(s):  
Chengjie Ji ◽  
Zhengping Wang ◽  
Liang Li
Keyword(s):  
Mass Spectrometry ◽  
Gel Electrophoresis ◽  
Protein Modification ◽  
Mass Spectrometric ◽  
Maldi Ms ◽  
Intact Protein ◽  
Protein Mass ◽  
Cell Extracts ◽  
Peptide Mass

A method for the characterization of modifications of low molecular weight proteins (<20 kDa) extracted from a microorganism based on the use of multiple separation tools and mass spectrometric techniques is described. In this method, intact proteins from cell extracts are first separated and fractionated by liquid chromatography (LC). Individual fractions are then analyzed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) to provide intact protein mass information. The fractions are further characterized by using trypsin digestion and LC electrospray ionization (ESI) MS/MS analysis of the resultant peptides to identify the proteins. Gel electrophoresis of a fraction is also carried out to estimate the molecular masses of the proteins. The gel bands are identified by in-gel digestion and peptide mass mapping and sequencing using MALDI-MS and MALDI-MS/MS. The combined information generated from these experiments is interpreted for detecting and characterizing modified proteins. This method has been developed and applied to the analysis of posttranslational modifications (PTMs) of low-mass proteins (5–20 kDa) extracted from a relatively well-characterized microorganism, Escherichia coli. Using this method, not only previously reported PTMs involving acetylation, methylation, oxidation, and the removal of signal peptides, but also two novel PTMs, namely loss of N-terminal Met-Thr-Met (MTM) and hydroxylation of arginine, were identified. It is envisaged that this method should be applicable to other relatively simple microorganisms for the discovery of new PTMs.Key words: top-down proteomics, protein modification, HPLC, gel electrophoresis, tandem mass spectrometry.

scholarly journals Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS

2019 ◽  
Vol 13 ◽  
pp. 117793221986822 ◽  
Author(s):  
Jean Lesne ◽  
Marie-Pierre Bousquet ◽  
Julien Marcoux ◽  
Marie Locard-Paulet
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Data Visualization ◽  
Web Application ◽  
Three Dimensional ◽  
Mass Spectrometry Data ◽  
Intact Protein ◽  
Top Down ◽  
Molecular Weights ◽  
Protein Mass

The rise of intact protein analysis by mass spectrometry (MS) was accompanied by an increasing need for flexible tools allowing data visualization and analysis. These include inspection of the deconvoluted molecular weights of the proteoforms eluted alongside liquid chromatography (LC) through their representation in three-dimensional (3D) liquid chromatography coupled to mass spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention times, and intensity of the MS signal). With this aim, we developed a free and open-source web application named VisioProt-MS ( https://masstools.ipbs.fr/mstools/visioprot-ms/ ). VisioProt-MS is highly compatible with many algorithms and software developed by the community to integrate and deconvolute top-down and intact protein MS data. Its dynamic and user-friendly features greatly facilitate analysis through several graphical representations dedicated to MS and tandem mass spectrometry (MS/MS) analysis of proteoforms in complex samples. Here, we will illustrate the importance of LC-MS map visualization to optimize top-down acquisition/search parameters and analyze intact protein MS data. We will go through the main features of VisioProt-MS using the human proteasomal 20S core particle as a user-case.

scholarly journals Intact protein mass spectrometry reveals intraspecies variations in venom composition of a local population of Vipera kaznakovi in Northeastern Turkey

2019 ◽  
Vol 199 ◽  
pp. 31-50 ◽  
Author(s):  
Daniel Petras ◽  
Benjamin-Florian Hempel ◽  
Bayram Göçmen ◽  
Mert Karis ◽  
Gareth Whiteley ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Local Population ◽  
Intact Protein ◽  
Protein Mass ◽  
Protein Mass Spectrometry ◽  
Venom Composition

Intact Protein Mass Spectrometry of Cell Culture Harvest Guides Cell Line Development for Trispecific Antibodies

2020 ◽  
Vol 92 (3) ◽  
pp. 2764-2769
Author(s):  
Fateme Tousi ◽  
Yan Jiang ◽  
Sharmila Sivendran ◽  
Yvonne Song ◽  
Susan Elliott ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cell Culture ◽  
Cell Line ◽  
Intact Protein ◽  
Cell Line Development ◽  
Protein Mass ◽  
Protein Mass Spectrometry

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’.

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