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|Abstract:||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.|
|Citation:||Baliban, Richard C., Peter A. DiMaggio, Mariana D. Plazas-Mayorca, Benjamin A. Garcia, and Christodoulos A. Floudas. "PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization." Journal of Proteome Research 11, no. 9 (2012): 4615-4629. doi: 10.1021/pr300418j|
|Pages:||4615 - 4629|
|Type of Material:||Journal Article|
|Journal/Proceeding Title:||Journal of Proteome Research|
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