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Backbone carbonyl group basicities are related to gas-phase fragmentation of peptides and protein folding
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
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2007 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 46, no 9, 1481-1484 p.Article in journal (Refereed) Published
Abstract [en]

A strong correlation is found between the propensity of individual amino acids to induce peptide-bond cleavage in the gas phase (PAA-XX) and their structure-forming propensity (PS, red) and H-bond-accepting propensity (PH, blue). Thus, the same fundamental parameter, carbonyl group basicity, governs the formation of secondary protein structures in solution and directs fragmentation in the gas phase. (Graph Presented).

Place, publisher, year, edition, pages
2007. Vol. 46, no 9, 1481-1484 p.
Keyword [en]
hydrogen bonds, mass spectrometry, peptide fragmentation, protein structures, proteomics
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-145840DOI: 10.1002/anie.200603881ISI: 000244507100023PubMedID: 17211901OAI: oai:DiVA.org:uu-145840DiVA: diva2:397027
Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2017-12-11Bibliographically approved
In thesis
1. New Proteomics Methods and Fundamental Aspects of Peptide Fragmentation
Open this publication in new window or tab >>New Proteomics Methods and Fundamental Aspects of Peptide Fragmentation
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Nya Proteomik Metoder och Fundamentala Aspekter av Peptid Fragmentering
Abstract [en]

The combination of collision-activated dissociation, (CAD) and electron capture dissociation, (ECD) yielded a 125% increase in protein identification. The S-score was developed for measuring the information content in MS/MS spectra. This measure made it possible to single out good quality spectra that were not identified by a search engine. Poor quality MS/MS data was filtered out, streamlining the identification process.

A proteomics grade de novo sequencing approach was developed enabling to almost completely sequence 19% of all MS/MS data with 95% reliability in a typical proteomics experiment.

A new tool, Modificomb, for identifying all types of modifications in a fast, reliable way was developed. New types of modifications have been discovered and the extent of modifications in gel based proteomics turned out to be greater than expected.

PhosTShunter was developed for sensitive identification of all phosphorylated peptides in an MS/MS dataset.

Application of these programs to human milk samples led to identification of a previously unreported and potentially biologically important phosphorylation site.

Peptide fragmentation has been studied. It was shown emphatically on a dataset of 15.000 MS/MS spectra that CAD and ECD have different cleavage preferences with respect to the amino acid context.

Hydrogen rearrangement involving z• species has been investigated. Clear trends have been unveiled. This information elucidated the mechanism of hydrogen transfer.

Partial side-chain losses in ECD have been studied. The potential of these ions for reliably distinguishing Leu/Iso residues was shown. Partial sidechain losses occurring far away from the cleavage site have been detected.

A strong correlation was found between the propensities of amino acids towards peptide bond cleavage employing CAD and the propensity of amino acids to accept in solution backbone-backbone H-bonds and form stable motifs. This indicated that the same parameter governs formation of secondary structures in solution and directs fragmentation in peptide ions by CAD.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 56 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 264
Keyword
Bioinformatics, Proteomics, Peptide fragmentation, Bioinformatik
Identifiers
urn:nbn:se:uu:diva-7438 (URN)978-91-554-6775-X (ISBN)
Public defence
2007-02-08, B21, BMC, Husargatan 3, Uppsala, 14:15
Opponent
Supervisors
Available from: 2007-01-17 Created: 2007-01-17 Last updated: 2013-09-04Bibliographically approved

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