Journal of Proteomics & Bioinformatics
Open Access

James C Wright

Publications

• Short Communication
  DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics
  Author(s): James C Wright and Jyoti S Choudhary James C Wright and Jyoti S Choudhary
  
  Accurate statistical evaluation of sequence database peptide identifications from tandem mass spectra is essential in mass spectrometry based proteomics experiments. These statistics are dependent on accurately modelling random identifications. The target-decoy approach has risen to become the de facto approach to calculating FDR in proteomic datasets. The main principle of this approach is to search a set of decoy protein sequences that emulate the size and composition of the target protein sequences searched whilst not matching real proteins in the sample. To do this, it is commonplace to reverse or shuffle the proteins and peptides in the target database. However, these approaches have their drawbacks and limitations. A key confounding issue is the peptide redundancy between target and decoy databases leading to inaccurate FDR estimation. This inaccuracy is further amplified at the.. View More»
  DOI: 10.4172/jpb.1000404

  Abstract PDF

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