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Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Ion Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Analytical Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Analytical Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Ion Physics.
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2002 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 74, no 22, 5826-5830 p.Article in journal (Refereed) Published
Abstract [en]

Liquid chromatography coupled on- or off-line with mass spectrometry is rapidly advancing as a tool in proteomics capable of dealing with the inherent complexity in biology and complementing conventional approaches based on two-dimensional gel electrophoresis. Proteins can be identified by proteolytic digestion and peptide mass fingerprinting or by searching databases using short-sequence tags generated by tandem mass spectrometry. This paper shows that information on the chromatographic behavior of peptides can assist protein identification by peptide mass fingerprinting in liquid chromatography/mass spectrometry. This additional information is significant and already available at no extra experimental cost.

Place, publisher, year, edition, pages
2002. Vol. 74, no 22, 5826-5830 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-89821DOI: 10.1021/ac0256890PubMedID: 12463368OAI: oai:DiVA.org:uu-89821DiVA: diva2:161606
Available from: 2002-04-23 Created: 2002-04-23 Last updated: 2017-12-14Bibliographically 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

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Ramström, MargaretaBergquist, Jonas

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