MRMPROBS suite for metabolomics using large-scale MRM assays

Hiroshi Tsugawa; Mitsuhiro Kanazawa; Atsushi Ogiwara; Masanori Arita

doi:10.1093/bioinformatics/btu203

MRMPROBS suite for metabolomics using large-scale MRM assays

Bioinformatics. 2014 Aug 15;30(16):2379-80. doi: 10.1093/bioinformatics/btu203. Epub 2014 Apr 20.

Authors

Hiroshi Tsugawa¹, Mitsuhiro Kanazawa², Atsushi Ogiwara², Masanori Arita¹

Affiliations

¹ 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.
² 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.

PMID: 24753485
DOI: 10.1093/bioinformatics/btu203

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.

Availability and implementation: MRMPROBS is available for Windows OS under the creative-commons by-attribution license at http://prime.psc.riken.jp.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Mass Spectrometry
Metabolomics / methods*
Software*