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Analytical utility of small neutral losses from reduced species in electron capture dissociation studied using SwedECD database
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
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2008 (English)In: Analytical Chemistry, ISSN 0003-2700, Vol. 80, no 21, 8089-8094 p.Article in journal (Refereed) Published
Abstract [en]

Small neutral losses from charge-reduced species [M + nH]((n-1)+center dot) is one of the most abundant fragmentation channels in both electron capture dissociation, ECD, and electron transfer dissociation, ETD. Several groups have previously studied these losses on particular examples. Now, the availability of a large (11491 entries) SwedECD database (http://www.bmms.uu.se/CAD/indexECD.html) of high-resolution ECD data sets on doubly charged tryptic peptides has made possible a systematic study involving statistical evaluation of neutral losses from [M + 2H](+center dot) ions. Several new types of losses are discovered, and 16 specific (>94%) losses are characterized according to their specificity and sensitivity, as well as occurrence for peptides of different lengths. On average, there is more than one specific loss per ECD mass spectrum, and two-thirds of all MS/MS data sets in SwedECD contain at least one specific loss. Therefore, specific neutral losses are analytically useful for improved database searching and de novo sequencing. In particular, N and GG isomeric sequences can be distinguished. The pattern of neutral losses was found to be remarkably dissimilar with the losses from radical z(center dot) fragment ions: e.g., there is no direct formation of w ions from the reduced species. This finding emphasizes the difference in fragmentation behaviors of hydrogen-abundant and hydrogen-deficient species.

Place, publisher, year, edition, pages
2008. Vol. 80, no 21, 8089-8094 p.
National Category
Pharmaceutical Sciences
URN: urn:nbn:se:uu:diva-97820DOI: 10.1021/ac800944uISI: 000260567000028OAI: oai:DiVA.org:uu-97820DiVA: diva2:172902
Available from: 2008-11-20 Created: 2008-11-20 Last updated: 2009-07-16Bibliographically approved
In thesis
1. Improved Neuropeptide Identification: Bioinformatics and Mass Spectrometry
Open this publication in new window or tab >>Improved Neuropeptide Identification: Bioinformatics and Mass Spectrometry
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bioinformatic methods were developed for improved identification of endogenous peptides using mass spectrometry. As a framework for these methods, a database for endogenous peptides, SwePep, was created. It was designed for storing information about endogenous peptides including tandem mass spectra. SwePep can be used for identification and validation of endogenous peptides by comparing experimentally derived masses of peptides and their fragments with information in the database. To improve automatic peptide identification of neuropeptides, targeted sequence collections that better mimic the peptidomic sample was derived from the SwePep database. Three sequence collections were created: SwePep precursors, SwePep peptides, and SwePep predicted. The searches for neuropeptides performed against these three sequence collections were compared with searches performed against the entire mouse proteome, and it was observed that three times as many peptides were identified with the targeted SwePep sequence collections. Applying the targeted SwePep sequence collections to identification of previously uncharacterized peptides yielded 27 novel potentially bioactive neuropeptides.

Two fragmentations studies were performed using high mass accuracy tandem mass spectra of tryptic peptides. For this purpose, two databases were created: SwedCAD and SwedECD for CID and ECD tandem mass spectra, respectively. In the first study, fragmentation pattern of peptides with missed cleaved sites was studied using SwedCAD. It was observed that peptides with two arginines positioned next to each other have the same ability to immobilize two protons as peptides with two distant arginines. In the second study, SwedECD was used for studying small neutral losses from the reduced species in ECD fragmentation. The neutral losses were characterized with regard to their specificity and sensitivity to function as reporter ions for revealing the presence of specific amino acids in the peptide sequence. The results from these two studies can be used to improve identification of both tryptic and endogenous peptides.

In summary, a collection of methods was developed that greatly improved the sensitivity of mass spectrometry peptide identification.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2008. 49 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, ISSN 1651-6192 ; 86
bioinformatics, neuropepides, database, peptide identification, peptide fragmentation, mass spectrometry, tandem mass spectromerty
National Category
Bioinformatics (Computational Biology)
urn:nbn:se:uu:diva-9400 (URN)978-91-554-7351-8 (ISBN)
Public defence
2008-12-12, B7:101a, B7, Husargatan 3, Uppsala, 10:15
Available from: 2008-11-20 Created: 2008-11-20Bibliographically approved

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