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Distinguishing and quantifying peptides and proteins containing D-amino acids by tandem mass spectrometry
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Technology, Department of Engineering Sciences.
In: Analytical Chemistry, ISSN 0003-2700, Vol. 77, no 14, 4571-4580 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Vol. 77, no 14, 4571-4580 p.
Identifiers
URN: urn:nbn:se:uu:diva-95863OAI: oai:DiVA.org:uu-95863DiVA: diva2:170225
Available from: 2007-05-07 Created: 2007-05-07Bibliographically approved
In thesis
1. Secondary and Higher Order Structural Characterization of Peptides and Proteins by Mass Spectrometry
Open this publication in new window or tab >>Secondary and Higher Order Structural Characterization of Peptides and Proteins by Mass Spectrometry
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies.

Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD.

Fragment ion abundances are a quantifiable tool providing chiral recognition (RChiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown.

The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding.

The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 58 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 304
Keyword
Engineering physics, Protein Structure, Mass Spectrometry, Electron Capture Dissociation, Tandem Mass Spectrometry, Teknisk fysik
Identifiers
urn:nbn:se:uu:diva-7861 (URN)978-91-554-6887-3 (ISBN)
Public defence
2007-05-28, B41, BMC, Husarg. 3, Uppsala, 10:15
Opponent
Supervisors
Available from: 2007-05-07 Created: 2007-05-07Bibliographically approved

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