Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Assessing the full information content of shotgun proteomics experiments has motivated a series of powerful bioinformatics advances. Here I present three bioinformatics tools for shotgun proteomics spectral identification and quality assessment. The IDBoost tool is a post-identification analysis tool that rescues spectral identifications and corrects identification errors by incorporating the relationships inferred through spectral clustering. The ScanRanker tool offers a way to recover unidentified high quality spectra for additional analysis via the assessment of tandem mass spectral quality. The QuaMeter tool focuses on the quality assessment of shotgun proteomics experiments and provides objective criteria for the evaluation of analytical system variability. Each tool was developed to solve one aspect of problems but together they work coordinately to provide an improved shotgun proteomics data analysis pipeline. The source code and binaries of these tools are available from http://fenchurch.mc.vanderbilt.edu/.
| Identifer | oai:union.ndltd.org:VANDERBILT/oai:VANDERBILTETD:etd-03222012-143216 |
| Date | 28 March 2012 |
| Creators | Ma, Zeqiang |
| Contributors | Daniel C. Liebler, David L. Tabb, Bing Zhang, Kathleen L. Gould, Zhongming Zhao |
| Publisher | VANDERBILT |
| Source Sets | Vanderbilt University Theses |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.library.vanderbilt.edu/available/etd-03222012-143216/ |
| Rights | restrictone, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Vanderbilt University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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