title: MRMPROBS suite for metabolomics using large-scale MRM assays.
abstract: We developed new software environment for the metabolome analysis of large-scale multiple reaction monitoring (MRM) assays. It supports the data format of four major mass spectrometer vendors and mzML common data format. This program provides a process pipeline from the raw-format import to high-dimensional statistical analyses. The novel aspect is graphical user interface-based visualization to perform peak quantification, to interpolate missing values and to normalize peaks interactively based on quality control samples. Together with the software platform, the MRM standard library of 301 metabolites with 775 transitions is also available, which contributes to the reliable peak identification by using retention time and ion abundances.
  
  
  METHODS
  MRMPROBS is available for Windows OS under the creative-commons by-attribution license at http://prime.psc.riken.jp.
authors.affiliation: RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan Reifycs Incorporated, 1-6-12 Nishishinbashi, Minato-ku, Tokyo 105-0003, Japan and National Institute of Genetics, Mishima, Shizuoka 411-8540, JapanRIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan Reifycs Incorporated, 1-6-12 Nishishinbashi, Minato-ku, Tokyo 105-0003, Japan and National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tsugawa
authors.affiliation: RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan Reifycs Incorporated, 1-6-12 Nishishinbashi, Minato-ku, Tokyo 105-0003, Japan and National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Kanazawa
authors.affiliation: RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan Reifycs Incorporated, 1-6-12 Nishishinbashi, Minato-ku, Tokyo 105-0003, Japan and National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Ogiwara
authors.affiliation: RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan Reifycs Incorporated, 1-6-12 Nishishinbashi, Minato-ku, Tokyo 105-0003, Japan and National Institute of Genetics, Mishima, Shizuoka 411-8540, JapanRIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan Reifycs Incorporated, 1-6-12 Nishishinbashi, Minato-ku, Tokyo 105-0003, Japan and National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
mesh_terms: D000465:Algorithms; D013058:Mass Spectrometry; D055432:Metabolomics / Q000379:methods*; D012984:Software