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Hydrogen Rearrangement to and from Radical z Fragments in Electron Capture Dissociation of Peptides
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.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
2007 (English)In: Journal of the American Society for Mass Spectrometry, ISSN 1044-0305, E-ISSN 1879-1123, Vol. 18, no 1, 113-120 p.Article in journal (Refereed) Published
Abstract [en]

Hydrogen rearrangement is an important process in radical chemistry. A high degree of H· rearrangement to and from z· ionic fragments (combined occurrence frequency 47% compared with that of z·) is confirmed in analysis of 15,000 tandem mass spectra of tryptic peptides obtained with electron capture dissociation (ECD), including previously unreported double H· losses. Consistent with the radical character of H· abstraction, the residue determining the formation rate of z′ = z· + H· species is found to be the N-terminal residue in z· species. The size of the complementary cm′ fragment turned out to be another important factor, with z′ species dominating over z· ions for m ≤ 6. The H· atom was found to be abstracted from the side chains as well as from α-carbon groups of residues composing the c′ species, with Gln and His in the c′ fragment promoting H· donation and Asp and Ala opposing it. Ab initio calculations of formation energies of ·A radicals (A is an amino acid) confirmed that the main driving force for H· abstraction by z· is the process exothermicity. No valid correlation was found between the N{single bond}Cα bond strength and the frequency of this bond cleavage, indicating that other factors than thermochemistry are responsible for directing the site of ECD cleavage. Understanding hydrogen attachment to and loss from ECD fragments should facilitate automatic interpretation ECD mass spectra in protein identification and characterization, including de novo sequencing.

Place, publisher, year, edition, pages
2007. Vol. 18, no 1, 113-120 p.
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-95357DOI: 10.1016/j.jasms.2006.09.008ISI: 000243712200014PubMedID: 17059886OAI: oai:DiVA.org:uu-95357DiVA: diva2:169534
Available from: 2007-01-17 Created: 2007-01-17 Last updated: 2017-12-14Bibliographically 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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