title: Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.
abstract: A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).
authors.affiliation: Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation.
authors.forename: Jingwen
authors.initials: J
authors.lastname: Yao
authors.affiliation: Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation.
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Utsunomiya
authors.affiliation: Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation.
authors.forename: Shigeki
authors.initials: S
authors.lastname: Kajihara
authors.affiliation: Biomarker & Personalized Medicine, Eisai Product Creation Systems.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tabata
authors.affiliation: Biomarker & Personalized Medicine, Eisai Product Creation Systems.
authors.forename: Ken
authors.initials: K
authors.lastname: Aoshima
authors.affiliation: Biomarker & Personalized Medicine, Eisai Product Creation Systems.
authors.forename: Yoshiya
authors.initials: Y
authors.lastname: Oda
authors.affiliation: Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation.
authors.forename: Koichi
authors.initials: K
authors.lastname: Tanaka
keywords: matrix-assisted laser desorption/ionization; peak detection; peptide identification; tandem mass spectrometry
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