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DE NOVO PEPTIDE SEQUENCING AND SPECTRAL ALIGNMENT ALGORITHM
VIA TANDEM MASS SPECTROMETRY
by
Lijuan Mo
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(COMPUTATIONAL BIOLOGY AND BIOINFORMATICS)
December 2009
Copyright 2009 Lijuan Mo
Object Description
| Title | De novo peptide sequencing and spectral alignment algorithm via tandem mass spectrometry |
| Author | Mo, Lijuan |
| Author email | lijuanmo@gmail.com; lijuanmo@usc.edu |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Computational Biology & Bioinformatics |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2009-06-02 |
| Date submitted | 2009 |
| Restricted until | Unrestricted |
| Date published | 2009-10-06 |
| Advisor (committee chair) | Chen, Ting |
| Advisor (committee member) |
Zandi, Ebrahim Alber, Frank |
| Abstract | Tandem mass spectrometry (MS/MS) has become an important experimental method for high throughput proteomics based biological discovery. The most common usage of MS/MS in biological applications is peptide sequencing. In this thesis, we focus on algorithms for MS/MS peptide identification and spectral alignment. We carry out two studies: (1) We have developed a de novo sequencing algorithm called MSNovo that integrates a new probabilistic scoring function with a mass array based dynamic programming algorithm. MSNovo works on various MS data generated from both LCQ and LTQ mass spectrometers and interprets singly, doubly and triply charged ions. MSNovo was tested to perform better than previous algorithms on several datasets. (2)We have developed a spectrum-peptide and spectrum-spectrum alignment algorithms called MSPEP. MSPEP identifies Post Translational Modifications through the spectrum-peptide alignment algorithm and reveals the relationship among unknown peptides through thespectrum-spectrum alignment algorithm. |
| Keyword | tandem mass spectrometry; mass spectrometry; de novo sequencing; spectral alignment; peptide sequencing; dynamic programing |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m2651 |
| Rights | Mo, Lijuan |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | http://www.usc.edu/isd/libraries/services/ask_a_librarian/email/ |
| Filename | etd-Mo-2918 |
| Archival file | uscthesesreloadpub_Volume48/etd-Mo-2918.pdf |
Description
| Title | Page 1 |
| Full text | DE NOVO PEPTIDE SEQUENCING AND SPECTRAL ALIGNMENT ALGORITHM VIA TANDEM MASS SPECTROMETRY by Lijuan Mo A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (COMPUTATIONAL BIOLOGY AND BIOINFORMATICS) December 2009 Copyright 2009 Lijuan Mo |
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