The Kazusa Metabolomics Portal



FragmentAlign is developed for data analyses of metabolome data obtained by gas chromatography (GC) - mass spectrometory (MS). The metabolites detected by electron ionization (EI) of GC-MS are observed as sets of ion products (fragments) which are specific to the originated metabolites. FragmentAlign compares the pattern of the ion fragments between the metabolite peaks observed in the different samples, aligns the peaks and then generates a data matrix which can be used as comparative analysis of metabolite amounts and multivariate analyses such as principal component analysis (PCA). By creating a data library of ion fragments of standard chemicals, the metabolite peaks detected by the same GC-MS instrument can be identified or annotated. FragmentAlign provides both of the functions for library construction and searching. One of unique functions of FragmentAlign is a powerful editing and correcting function of the alignment results, which facilitates researchers to prepare curated data matrices for further careful investigations of the metabolome data. The alignment data created by the other tools can be imported into FragmentAlign to edit and refine the alignment results. The tool is designed to accept text-formatted file as input, enables to process data of any GC-MS instruments as long as the data can be converted to the defined text format.

Download :

FragmentAlign 1.18.1 (1.82 MB)

Manual (1.66 MB)

Tutorial Data 1.0 (9.53 MB)

The previous version named "Metabolometrics" (1.30 MB)

* Click once and wait for a while. Due to the security checking system of the server, it may take ~90 seconds to start downloading.


FragmentAlign has been tested under following environment. Java Runtime Environment (1.6 or later) is required.

OS: Windows XP / Vista / 7 (32 bit), 7 (64 bit) 
Software: Java Runtime Environment (JRE 1.6.0_14)


KOMICS Wikiサイトに順次追加してゆきます。




Sakurai N, Ara T, Enomoto M, Motegi T, Morishita Y, Kurabayashi A, Iijima Y, Ogata Y, Nakajima D, Suzuki H, and Shibata D (2014) Tools and Databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. BioMed Research International, 2014: 194812



Contact Information :

Nozomu Sakurai, e-mail: sakurai AT kazusa.or.jp


This software is academic free, and is not allowed to use for commercial purpose.