title: Target-Decoy with Mass Binning: a simple and effective validation method for shotgun proteomics using high resolution mass spectrometry.
abstract: Shotgun proteomics using mass spectrometry (MS) has become the choice for large-scale peptide and protein identification. The recent development of high-resolution mass spectrometers such as FT-ICR or Orbitrap makes it possible to identify peptides within only a few parts per million (ppm), and it is expected to dramatically improve performance of peptide identification, as compared to low-resolution instruments. To fully exploit such significantly higher mass accuracy, however, appropriate data analysis methods are required. Here, we present a new target-decoy strategy, called Target-Decoy with Mass Binning, utilizing high mass accuracy for peptide identification validation, which remains a challenging problem in MS-based proteomics. When tested on various high-resolution MS data, our method was very effective and yet simple and showed comparable or better performance when compared with other validation methods.
authors.affiliation: Korea Institute of Science and Technology, Seoul, Republic of Korea.
authors.forename: Jong Wha J
authors.initials: JW
authors.lastname: Joo
authors.forename: Seungjin
authors.initials: S
authors.lastname: Na
authors.forename: Je-Hyun
authors.initials: JH
authors.lastname: Baek
authors.forename: Cheolju
authors.initials: C
authors.lastname: Lee
authors.forename: Eunok
authors.initials: E
authors.lastname: Paek
mesh_terms: D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics