title: Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics.
abstract: BACKGROUND
  In proteomic analysis, MS/MS spectra acquired by mass spectrometer are assigned to peptides by database searching algorithms such as SEQUEST. The assignations of peptides to MS/MS spectra by SEQUEST searching algorithm are defined by several scores including Xcorr, Delta Cn, Sp, Rsp, matched ion count and so on. Filtering criterion using several above scores is used to isolate correct identifications from random assignments. However, the filtering criterion was not favorably optimized up to now.
  
  
  RESULTS
  In this study, we implemented a machine learning approach known as predictive genetic algorithm (GA) for the optimization of filtering criteria to maximize the number of identified peptides at fixed false-discovery rate (FDR) for SEQUEST database searching. As the FDR was directly determined by decoy database search scheme, the GA based optimization approach did not require any pre-knowledge on the characteristics of the data set, which represented significant advantages over statistical approaches such as PeptideProphet. Compared with PeptideProphet, the GA based approach can achieve similar performance in distinguishing true from false assignment with only 1/10 of the processing time. Moreover, the GA based approach can be easily extended to process other database search results as it did not rely on any assumption on the data.
  
  
  CONCLUSIONS
  Our results indicated that filtering criteria should be optimized individually for different samples. The new developed software using GA provides a convenient and fast way to create tailored optimal criteria for different proteome samples to improve proteome coverage.
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China. vext@dicp.ac.cn
authors.forename: Xinning
authors.initials: X
authors.lastname: Jiang
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Jiang
authors.forename: Guanghui
authors.initials: G
authors.lastname: Han
authors.forename: Mingliang
authors.initials: M
authors.lastname: Ye
authors.forename: Hanfa
authors.initials: H
authors.lastname: Zou
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D020543:Proteome