PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization
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- 作者：Richard C. Baliban ; Peter A. DiMaggio ; Mariana D. Plazas-Mayorca ; Benjamin A. Garcia ; Christodoulos A. Floudas
- 刊名：Journal of Proteome Research
- 出版年：2012
- 出版时间：September 7, 2012
- 年：2012
- 卷：11
- 期：9
- 页码：4615-4629
- 全文大小：608K
- 年卷期：v.11,no.9(September 7, 2012)
- ISSN：1535-3907
文摘
A novel protein identification framework, PILOT_PROTEIN, has been developed to construct a comprehensive list of all unmodified proteins that are present in a living sample. It uses the peptide identification results from the PILOT_SEQUEL algorithm to initially determine all unmodified proteins within the sample. Using a rigorous biclustering approach that groups incorrect peptide sequences with other homologous sequences, the number of false positives reported is minimized. A sequence tag procedure is then incorporated along with the untargeted PTM identification algorithm, PILOT_PTM, to determine a list of all modification types and sites for each protein. The unmodified protein identification algorithm, PILOT_PROTEIN, is compared to the methods SEQUEST, InsPecT, X!Tandem, VEMS, and ProteinProspector using both prepared protein samples and a more complex chromatin digest. The algorithm demonstrates superior protein identification accuracy with a lower false positive rate. All materials are freely available to the scientific community at http://pumpd.princeton.edu.