uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Automatic Analysis of Hydrogen/Deuterium Exchange Mass Spectra of Peptides and Proteins using Calculations of Isotopic Distributions
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Materials Science.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Surface Biotechnology.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Ion Physics.
2001 (English)In: Journal of the American Society for Mass Spectrometry, ISSN 1044-0305, E-ISSN 1879-1123, Vol. 12, no 11, 1153-1162 p.Article in journal (Refereed) Published
Abstract [en]

High mass-resolving power has been shown to be useful for studying the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange. A computer algorithm was developed that automatically identifies peptides and their extent of deuterium incorporation from H/D exchange mass spectra of enzymatic digests or fragment ions produced by collisionally induced dissociation (CID) or electron capture dissociation (ECD). The computer algorithm compares measured and calculated isotopic distributions and uses a fast calculation of isotopic distributions using the fast Fourier transform (FFT). The algorithm facilitates rapid and automated analysis of H/D exchange mass spectra suitable for high-throughput approaches to the study of peptide and protein structures. The algorithm also makes the identification independent on comparisons with undeuterated control samples. The applicability of the algorithm was demonstrated on simulated isotopic distributions as well as on experimental data, such as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin peptic digests, and CID and ECD spectra of substance P.

Place, publisher, year, edition, pages
2001. Vol. 12, no 11, 1153-1162 p.
National Category
Natural Sciences Engineering and Technology
Identifiers
URN: urn:nbn:se:uu:diva-89823DOI: 10.1016/S1044-0305(01)00301-4PubMedID: 11720389OAI: oai:DiVA.org:uu-89823DiVA: diva2:161608
Available from: 2002-04-23 Created: 2002-04-23 Last updated: 2013-06-13Bibliographically approved
In thesis
1. Identification and Characterization of Peptides and Proteins using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Open this publication in new window or tab >>Identification and Characterization of Peptides and Proteins using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
2002 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2002. 76 p.
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 706
Keyword
Materials science, Peptide, protein, peptide mass fingerprinting, identification, sequencing, protein structure, non-covalent interaction, modification, electrospray ionization, liquid chromatography, capillary electrophoresis, electron capture dissociation, Fourier transform ion cyclotron resonance mass spectrometry, cerebrospinal fluid, amyloid β-peptide, Alzheimer’s disease., Materialvetenskap
National Category
Materials Engineering
Research subject
Molecular Biotechnology
Identifiers
urn:nbn:se:uu:diva-1999 (URN)91-554-5296-5 (ISBN)
Public defence
2002-05-17, Siegbahnsalen, Uppsala, 10:00 (English)
Opponent
Available from: 2002-04-23 Created: 2002-04-23 Last updated: 2010-01-14Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed
By organisation
Department of Materials ScienceSurface BiotechnologyIon Physics
In the same journal
Journal of the American Society for Mass Spectrometry
Natural SciencesEngineering and Technology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 505 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf