Spectral counting has become a widely used approach for comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly affects the assessment of peptide and protein differentiation. Meanwhile, the configuration of database searching algorithms that assign peptides to MS/MS spectra may produce different results. Here, I present three strategies to improve comparative proteomics through spectral counting. I show that comparing spectral counts for peptide groups rather than for protein groups forestalls problems introduced by shared peptides. I present four models to combine four popular search engines that lead to significant gains in spectral counting differentiation. Among these models, I demonstrate a powerful vote counting model that scales well for multiple search engines. I also show that semi-tryptic searching outperforms tryptic searching for comparative proteomics. Overall, these techniques considerably improve protein differentiation on the basis of spectral count tables.
| Identifer | oai:union.ndltd.org:VANDERBILT/oai:VANDERBILTETD:etd-05152012-120718 |
| Date | 15 May 2012 |
| Creators | Chen, Yao-Yi |
| Contributors | Ming Li, Bing Zhang, David L. Tabb |
| 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-05152012-120718/ |
| Rights | unrestricted, 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. |
Page generated in 0.2797 seconds