JDAMP

About

JDAMP (Java application for Differential Analysis of Metabolite Profiles) is a collection of easy-to-use tools for analyzing capillary electrophoresis-mass spectrometry (CE-MS) data.

This software subtracts background drifts, removes noise, aligns datasets, and vidualizes significant differences among multiple runs.

News

14/Dec/2011 JDAMP ver. 1.4.1 was released. - Launching way was changed. Use JDAMP_500M.vbs instead of JDAMP.exe. The function about exporting csv file was improved. The issue of ciff file converted from .D data was fixed.

12/Dec/2011 dotMZ ver. 1.1.1.2 was released. - Time-segment handling was improved.

2/Oct/2009 A link for JDAMP publication was uploaded.

1/Jul/2009 dotMZ ver. 1.0.0.9 were released. Bugfix - When multiple CPUs were used temporary files were conflicted.

25/Jun/2009 JDAMP ver. 1.3.4 and dotMZ ver. 1.0.0.8 were released and installation of this page was updated.

JDAMP 1.3.4 - Normalized binned electropherograms, matrix of detected differences with normalized intensities can be exported as csv format.

dotMZ 1.0.0.8 - .D data (MassHunter, Agilent), txt file (MassLynx, Waters), NetCDF (tested on AnalystQS and MassHunter) can be imported. The kiff file as well as ciff can be exported but still only ciff can be used for JDAMP input.

20/Jan/2009 JDAMP ver 1.3.2 was uploaded. Buxfix about internal standard selection.

3/Dec/2008 JDAMP ver 1.3.1, JDAMP-A ver 1.0.1, and English manual were uploaded.

24/Feb/2008 Japanese manual of dotMZ was uploaded.

12/Feb/2008 File description documents were added. Manuals were updated.

27/Feb/2008 Install description was edited.

20/Feb/2008 Movie pages were updated.

13/Feb/2008 Newly opened.

Download

dotMZ ver.1.1.1.2 (4.5M) [zip] File converter for exporting JDAMP (JDAMP-A) input files.

JDAMP ver.1.4.1 (3.5M) [zip] Differential detection tool for datapoint-and-datapoint basis algorithm.

JDAMP-A ver.1.0.1 (3.5M) [zip] Differential detection tool for area basis algorithm.

Get old version

JDAMP and JDAMP-A were currently released separately because the table columns and the information displayed in electropherograms are completely different (However, they will be integrated). JDAMP provides datapoint-by-datapoint difference detection with Gaussian filtering. Although JDAMP also retain the function to sort the results according to averaged peak area, the area is simply calculated by the Gaussian to be fit. Use JDAMP-A for more sophisticated area detection. Because not only ciff files (input files) but also bdt files (noise reduced files) can be shared by both tools, noise reduction process that is the most time consuming should be conducted once at least.

Install

Java 6 and Microsoft .NET Framework 3.0 SP1 (or 3.5) are necessary for both JDAMP and dotMZ.

1. Download Java Runtime Engironment (JRE) 6 and Install it. If JDK is already installed, JRE is not necessary

2. Download Microsoft .NET Framework 3.0 (SP1) Redistributable Package and install it. If your PC is not updated, the installation of .Net Framework 2.0 and Windows Installer is required precedently. In order to install .NET Framework 3.0 SP1, execute Windows Update through Internet Explorer. Otherwise install Microsoft .NET Framework 3.5 instead of 3.0 SP1.

Installation of AnalystQS or MassHunter for Agilent TOF is required only if you convert Agilent wiff file to ciff file by dotMZ. CSV file, txt file, NetCDF can be converted by dotMZ without these vender-supplied software.

To get AnalystQS for Agilent TOF or MassHunter, contact to Agilent.

For instllation of AnalystQS or MassHunter, execute Setup.exe file in the resolved AnalystQS directory and follow the instructions on the screen. Select Only for AnalystQS, "Processing Mode" in a mode selection window during installing. In addition only for AnalystQS, you have to configurate AnalystQS or additionally install G3300AA TOF Softoware for using AnalystQS's API. Follow the AnalystQS's manual or contact to Agilent how to obtain the module.

Movies

You can quickly learn how to use JDAMP. Adobe Flash player is required to watch the movies.

- dotMZ (X MB) file convertion[link] (still under preparing)

- JDAMP part 1. (4MB) Start up to time-alignment [link]

- JDAMP part 2. (6.5MB) Normalization to visualize analysed results [link]

Documentation

How to install, quick tutorial, operating manual, and FAQ is described.

- Installation manual(for all software) [English] [Japanese]

- DotMZ manual [English] [Japanese]

- JDAMP manual [English] [Japanese]

- File description/System requirements/Performancs

Examples

You can start JDAMP with example files. Datasets of 2 groups (n=3) are available here.

DotMZ imports Agilent wiff files or CSV files and exports ciff files. If you want to try JDAMP only, download ciff files or BDT files.

BDT files are intermediate file of which noise is removed from ciff files. If you import BDT files by JDAMP, you can skip noise-filtering process.

Agilent wiff files. (about 100MB x 6)

- WT_1.wiff - WT_2.wiff - WT_3.wiff

- KO_1.wiff - KO_2.wiff - KO_3.wiff

CSV files (about 900MB x 6)

- WT_1.csv - WT_2.csv - WT_3.csv

- KO_1.csv - KO_2.csv - KO_3.csv

ciff files (Converted data files by dotMZ) (about 100MB x 6)

- WT_1.ciff - WT_2.ciff - WT_3.ciff

- KO_1.ciff - KO_2.ciff - KO_3.ciff

BDT files (Noise removed files) (about 25MB x 6)

- WT_1.bdt - WT_2.bdt - WT_3.bdt

- KO_1.bdt - KO_2.bdt - KO_3.bdt

known compound list. (cation)

- cation_list.csv

The file contains a list of m/z values, migration times, indexs (sequential integer number), names, and comment.

References

Sugimot, M. et al. (2009) Differential metabolomics software for capillary electrophoresis-mass spectrometry data analysis Metabolomics 10.1007/s11306-009-0175-1 [link]

Baran, R. et al. (2006) MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics 7: 530 [link]

Baran, R. et al. (2007) Visualization of three-way comparisons of omics data. BMC Bioinformatics 8:72 [link]

MathDamp web site [link]

Contact

Please give any feedback and requirement to Masahiro SUGIMOTO (msugi at sfc.keio.ac.jp).

Research Associate, Institute for Advanced Biosciences, Keio University

Tsuruoka Metabolome Campus 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052 Japan

Tel:+81-235-29-0528 Fax:+81-235-29-0574

Old version

DotMZ ver.1.0.0.1 (3.5M) [zip]

DotMZ ver.1.0.0.8 (4.3M) [zip]

DotMZ ver.1.0.0.9 (4.3M) [zip]

JDAMP ver.1.2.8 (3.5M) [zip]

JDAMP ver.1.3.1 (3.5M) [zip]

JDAMP ver.1.3.2 (3.5M) [zip]

JDAMP ver.1.3.3 (3.5M) [zip]

JDAMP ver.1.3.4 (3.5M) [zip]