Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA.
J Proteome Res. 2012 Sep 7;11(9):4615-29. doi: 10.1021/pr300418j. Epub 2012 Jul 26.
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.
已开发出一种新的蛋白质鉴定框架 PILOT_PROTEIN，用于构建存在于生物样本中的所有未经修饰蛋白质的综合清单。它使用 PILOT_SEQUEL 算法的肽鉴定结果初步确定样本中的所有未经修饰蛋白质。通过使用严格的双聚类方法将不正确的肽序列与其他同源序列分组，最大限度地减少报告的假阳性数量。然后，将序列标记程序与非靶向 PTM 鉴定算法 PILOT_PTM 结合使用，以确定每种蛋白质的所有修饰类型和位置的列表。使用预制蛋白质样本和更复杂的染色质消化物，将未经修饰的蛋白质鉴定算法 PILOT_PROTEIN 与 SEQUEST、InsPecT、X!Tandem、VEMS 和 ProteinProspector 进行比较。该算法具有较低的假阳性率，显示出更高的蛋白质鉴定准确性。所有材料均可在 http://pumpd.princeton.edu 上免费提供给科学界。
