scholarly journals Quantitative Mass Spectrometry-Based Proteomics: An Overview

2021 ◽  
pp. 85-116
Author(s):  
Svitlana Rozanova ◽  
Katalin Barkovits ◽  
Miroslav Nikolov ◽  
Carla Schmidt ◽  
Henning Urlaub ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Front Line ◽  
Quantitative Mass Spectrometry ◽  
Qualitative Level ◽  
The Common ◽  
Challenging Question ◽  
Further Development ◽  
Proteins And Peptides

AbstractIn recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.

scholarly journals Labeled quantitative mass spectrometry to study the host response during aspergillosis in the common bottlenose dolphin (Tursiops truncatus)

2019 ◽  
Vol 232 ◽  
pp. 42-49
Author(s):  
Guillaume Desoubeaux ◽  
Maria del Carmen Piqueras ◽  
Carolina Le-Bert ◽  
Vanessa Fravel ◽  
Tonya Clauss ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Bottlenose Dolphin ◽  
Tursiops Truncatus ◽  
Host Response ◽  
Quantitative Mass Spectrometry ◽  
Common Bottlenose Dolphin ◽  
The Common

scholarly journals De novo sequencing of proteins and peptides: algorithms, applications, perspectives

2018 ◽  
Vol 1 (1) ◽  
pp. e00005 ◽  
Author(s):  
K.V. Vyatkina
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Database Search ◽  
Mass Spectrometric ◽  
Spectrometric Measurements ◽  
Further Development ◽  
Structure Of Proteins ◽  
Proteins And Peptides

Determination of the primary structure of proteins and peptides constitutes an important step in studying their properties. Currently, mass spectrometry is commonly applied to this end. The results of mass spectrometric measurements can be interpreted by means of either a database search or de novo sequencing methods. The appeal of the latter is due to their applicability to investigating unknown proteins, as well as the ones that cannot be analyzed with genomics or transcriptomics methods. In this paper, we briefly review the existing approaches to de novo sequencing of proteins and peptides, along with the problems that can be solved using those, and indicate directions and perspectives for their further development.

Quantitative analysis of multiple high-resolution mass spectrometry images using chemometric methods: quantitation of chlordecone in mouse liver

The Analyst ◽  
2018 ◽  
Vol 143 (10) ◽  
pp. 2416-2425 ◽  
Author(s):  
Saeedeh Mohammadi ◽  
Hadi Parastar
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
High Resolution ◽  
Mouse Liver ◽  
Mass Spectrometry Imaging ◽  
High Resolution Mass Spectrometry ◽  
Chemometric Methods ◽  
Quantitative Mass Spectrometry ◽  
High Resolution Mass ◽  
Resolution Mass

In this work, a chemometrics-based strategy is developed for quantitative mass spectrometry imaging (MSI).

scholarly journals Single Quadrupole Multiple Reaction Monitoring Q-MRM enables Quantitative Mass Spectrometry

2021 ◽  
Author(s):  
Jingchuan Xue ◽  
Rico J.E. Derks ◽  
William Wwebb ◽  
Aries Aisporna ◽  
Martin Giera ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Matrix Effects ◽  
Multiple Reaction Monitoring ◽  
Mass Spectrometry Analysis ◽  
Good Precision ◽  
Reaction Monitoring ◽  
Font Size ◽  
Quantitative Mass Spectrometry ◽  
Fragment Ions

<p> </p><p>A single quadrupole combined with enhanced in-source fragmentation/annotation (EISA) was used to perform multiple reaction monitoring (Q-MRM) for quantitative mass spectrometry analysis. EISA amplifies fragmentation of traditional soft electrospray ionization to produce fragment ions that have been found to be identical to those generated in tandem mass spectrometry. We have combined EISA fragmentation data with criteria established by the European Union Commission Directive 2002/657/EC for electron ionization single quadrupole quantitative analysis to perform quantitative Q-MRM experiments. These experiments were performed on multiple types of complex samples that included a mixture of 50 standards, as well as cell and plasma extracts. The dynamic range for Q-MRM quantitative analysis was comparable to triple quadrupole multiple reaction monitoring (QqQ-MRM) analyses at up to 5 orders of magnitude with the cell and plasma extracts showing similar matrix effects across both platforms. Amino acid and fatty acid measurements performed from certified NIST 1950 plasma with isotopically labelled standards demonstrated Q-MRM accuracy in the range of 91-110% for the amino acids, 76-129% for the fatty acids, and good precision (coefficient of variation < 10%). In order to enhance specificity, a newly developed Correlated Ion Monitoring (CIM) algorithm was designed to facilitate these analyses. CIM autonomously processes, aligns, filters, and compiles multiple ions within one chromatogram enabling both precursor and in-source fragment ions to be correlated within a single chromatogram, also enabling the detection of co-eluting species based on precursor and fragment ion ratios. Q-MRM and CIM with single quadrupole instrumentation has been designed as an alternative to QqQ-MRM technology by correlating precursor and fragment ions to facilitate high sensitivity Q-MRM quantitative analysis on existing instrumentation that are generally inexpensive, easy to operate, and technically less complex. </p> <p>@font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:3 0 0 0 1 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman";}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-size:11.0pt; mso-ansi-font-size:11.0pt; mso-bidi-font-size:11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:DengXian; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi; mso-fareast-language:ZH-CN;}.MsoPapDefault {mso-style-type:export-only; margin-bottom:8.0pt; line-height:107%;}div.WordSection1 {page:WordSection1;}</p>

scholarly journals Once again about the prophetic mission of the Russian writer (based on material of Y.V. Bondarev’s novel “The Shore”)

Neophilology ◽  
2021 ◽  
pp. 661-669
Author(s):  
Liudmila E. Khvorova
Keyword(s):  
The Novel ◽  
Front Line ◽  
Cultural Foundations ◽  
Great Patriotic War ◽  
Russian Literary ◽  
The Common ◽  
German City ◽  
Prophetic Mission ◽  
Literary Classics ◽  
Further Development

We conduct continuous poetical and philosophical research on the work of Y.V. Bondarev (1924–2020), the greatest Russian Soviet prose writer and a participant in the Great Patriotic War. Based on the study of the novel “The Shore” (1975) and the writer’s journalistic statements of the mid-1970s of the 20th century, within the framework of cultural-axiological paradigm, we attempt to comprehend one of the central dialogues between representatives of the creative intellectuals of Russia and West. The conversation between Russian Soviet writer Nikitin, a former front-line soldier who visited the German city of Hamburg 26 years after the war, and the German journalist and publisher Dietzman is read as a kind of philosophical quintessence of both this novel and, possibly, the writer’s work as a whole. The conflict between Russia and West is seen by Y.V. Bondarev in the most complex metaphysical paradigm of the struggle of largely opposite cultural foundations, despite the common Christian basis. We state the complexity, multidimensionality, polyphonism of the Bondarev type of artistic expression, its ascent to the traditions of Russian literary classics and, above all, in this case to the work of F.M. Dostoevsky. We note the key, culminating significance of this dialogue-reflection undertaken in the chapter of the second chapter of the third part “Nostalgia” by Dietzman and Nikitin, which has some obvious similarities with the author both for the further development of latter’s character in the poetical and philosophical space of novel, and for its artistic “completion” in work finale. We comprehend the relevance of Bondarev’s metaphysical constants in the first quarter of the 21st century, prophetically written out about half a century ago.

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.

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