MsdialWorkbench contents

MS-DIAL - software for untargeted metabolomics and lipidomics

The program supports data processings for any type of chromatography / scan type mass spectrometry data, and the assembly is licensed under the CC-BY 4.0.

MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rules

The program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.

From e-mail to GitHub (for open science)

If you would like to discuss with us (for feedback, bug reports, and questions), we would appreciate it if you could do it on https://github.com/systemsomicslab/MsdialWorkbench/issues or https://github.com/systemsomicslab/MsdialWorkbench/discussions (instead of e-mail).

However, if the discussion is something that cannot be done openly by any means, please email msdial-jp-groups@go.tuat.ac.jp.

How to build MS-DIAL5 Desktop Application (for Windows)

Installing Visual Studio and cloning MsdialWorkbench source code

Download and install Visual Studio Community 2022. (In the Workloads selection, choose .NET desktop development. )
Git clone this repo with git clone https://github.com/mtbinfo-team/MsdialWorkbench.

Building MsdialWorkbench with Visual Studio

Double click MsdialWorkbench.sln in the cloned repo.
Right-click on MsdialWorkbench in the Solution Explorer.
Click Manage NuGet Packages for Solution....
Add the Assemblies folder in this repo to the Package source:.
Select Debug vendor unsupported from the Solution Configurations pull-down menu.
Select MsdialGuiApp from the Startup Projects pull-down menu.
Click ▶ MsdialGuiApp button on the right side of 8.

Developers

Lead developer: Hiroshi Tsugawa (TUAT/RIKEN)

Current main developers: Hiroshi Tsugawa (TUAT/RIKEN), Mikiko Takahashi (RIKEN), and Yuki Matsuzawa (TUAT)

Past developers: Diego Pedrosa (UC Davis), Ipputa Tada (SOKENDAI)

Usage

See the tutorial page: https://systemsomicslab.github.io/mtbinfo.github.io/

About LBM file in MS-DIAL project

The LBM (*.LBM2) file contains the in silico MS/MS spectra of lipids. There are currently three files named with 'FiehnO (Oliver Fiehn laboratory)', 'AritaM (Makoto Arita laboratory)', and 'SaitoK (Kazuki Saito laboratory)'. These files contain the same MS/MS spectra information but have different predicted retention times which were optimized for the indivisual method. One of the '.LBM' files which contains lipid's in silico MS/MS should be also in the same folder as 'MSDIAL.exe' for Lipidomics project.

Further

MRMPROBS software suite is sutable for targeted metabolomics and lipidomics, and it also supports MRM/SRM data. http://prime.psc.riken.jp/compms/mrmprobs/main.html

Source code license

The source code is licensed under GNU LESSER GENERAL PUBLIC LICENSE (LGPL) version 3. See LGPL.txt for full text of the license. This software uses third-party software. A full list of third-party software licenses in MsdialWorkbench is in the file THIRD-PARTY-LICENSE-README.txt.