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dc.contributor.advisorAllmer, Jensen
dc.contributor.authorAytun, Belginen
dc.date.accessioned2014-07-22T13:50:51Z
dc.date.available2014-07-22T13:50:51Z
dc.date.issued2011en
dc.identifier.urihttp://hdl.handle.net/11147/3089
dc.descriptionThesis (Master)--Izmir Institute of Technology, Molecular Biology and Genetics, Izmir, 2011en
dc.descriptionIncludes bibliographical references (leaves: 58-64)en
dc.descriptionText in English; Abstract: Turkish and Englishen
dc.descriptionx, 64 leavesen
dc.description.abstractPeptide identification from mass spectrometric data is a key step in proteomics because this field provides sequence, quantitative, and modification data of actually expressed proteins. Two approaches are generally deployed to interpret experimental MS/MS data, database searching and de novo sequencing. Database search method has been used successfully in proteomics projects for organisms with well-studied genomes. However, it is not applicable in situations where a target sequence is not in the protein database. This can happen for a number of reasons, including novel proteins, protein mutations and post-translational modifications. Because of the disadvantages of database searching method, a lot of research has focused on de novo sequencing method which assigns amino acid sequences to MS/MS spectra without the need for a database. The aim of this study is to enhance the accuracy of de novo sequencing tools. One step commonly employed in all de novo sequencing tools is naming of fragment ions. It is essential to know which peak represents which ion type in order to traverse a spectrum graph to find an amino acid sequence that best explains the MS/MS spectrum. Different approaches have been tried to name ions and some success has been achieved in naming b-type ions and y-type ions. We have presented a new approach which enables the naming of not only b- and y-type ions but other arbitrary ion types as well. This enabled the detection of b-ion ladder. In the latter case, missing fragments were determined by using other named ion types. Furthermore, unexplained data in tandem mass spectra were reduced as much as possible. Therefore, a complete sequence will be derived by the new approach.en
dc.language.isoengen
dc.publisherIzmir Institute of Technologyen
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subject.lcshMass spectrometryen
dc.subject.lcshTandem mass spectrometryen
dc.subject.lcshProteomicsen
dc.subject.lcshPeptidesen
dc.titleExploiting fragment-ion complementarity for peptide de novo sequencing from collision induced dissociation tandem mass spectraen
dc.typemasterThesisen
dc.contributor.departmentIzmir Institute of Technology. Molecular Biology and Geneticsen
dc.relation.publicationcategoryTezen_US


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