Idfraip: A Novel Protein Identification Algorithm Based On Fragment Intensity Patterns

Identifying peptides for their fragmentation spectra by database search sequencing method is crucial to interpret LC-MS/MS data, widely used algorithms had not been fully exploited the intensity patterns in fragment spectra, SQID incorporated intensity information and identified peptides significantly more peptides than Sequest and X!Tandem. Although SQID adopted various datasets which based on different platforms to show its robustness and effectiveness, many other characterizes were not considered. This article utilized intensity pattern modeling which had been reported by SQID, proposed a novel scoring model to identify fragment spectra. Compared with SQID and Sequest at 1% False Discovery Rate (FDR), IDFraIP identified more confident peptides and spectra.