MS-DIAL

Program download

MS-DIAL main program: Download
MS-DIAL tutorial: Link
MS-DIAL forum: Link
MS-DIAL console application tutorial: Link
The tutorials and parameter files for MS-DIAL AIF data processing and spectral library construction methogology: Download
Lipid nomenclature in MS-DIAL lipidomics: Link
Annotation 'code' of compound identification and annotation confidence in MS-DIAL metabolomics/lipidomics: Link
Abf file converter: Link
FAQ for MS-DIAL and ABF file converter: Link
MS-DIAL mathematics: Download
The core source code of MS-DIAL: Download

Library templates

See below for MSP format files.
Text format library for metabolite identifications. Template
SWATH-MS experiment file. Template.
All-ions experiment file (MSE, all-ions, all ion fragmentations etc). Template
Multiple CEs all-ions experiment file. Template.
Reference library for diagnostic marker ions for retention time correction in LC-MS projects. Template.
Peak list file for merging different polarity ions (e.g. in negative ion mode) to determine the adduct type (e.g. in positive ion mode).Template
Text format library for metabolite identifications using CCS. Pos template and Neg template
(For CCS resources, see AllCCS database and PNNL CCS database).

Objective

MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters). Common data formats such as netCDF (AIA) and mzML, can also be managed in our project. In addition, we released several MSP files including both EI- and MS/MS spectra as a ‘start-up kit’. Moreover, MS-DIAL internally has a version of Fiehn lab’s GC/MS database (oriented by FAME RI index), and in silico retention time- and MS/MS database for LC/MS/MS based lipidomics. The isotope labeled tracking can also be executed in LC/MS project. It features (1) spectral deconvolution for both GC/MS and data-independent MS/MS, (2) streamlined criteria for peak identification, (3) support of all data processing steps from raw data import to statistical analysis, and (4) user-friendly graphic user interface.

Please cite

  • DIA-MS and Lipidomics: MS-DIAL: data independent MS/MS deconvolution for comprehensive metabolome analysis. Nature Methods, 12, 523-526, 2015 [PubMed]
  • GC-MS project: Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods, 15, 53-56, 2018 [NPG link]
  • General and plant metabolomics: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods, 16, 295-298, 2019 [NPG link]
    Springer Nature 'SharedIt': full-text access to a view-only version of this paper

Demonstration files

LC-MS/MS data set (.wiff and .wiff.scan, and the converted abf files) for lipid profiling of algae is available from here. Download; Also see MSDIAL quick start
LC-MS/MS data set (.abf, data dependent MS/MS acquisition) for hydrophilic metabolome profiling of Wine is available from here. Download;
GC-MS data set (.cdf and .abf files) for small biomolecule analysis of Arabidopsis thaliana and Alage is available from here. Download;
HILIC-SWATH-MS data (.wiff, .wiff.scan, and .abf) that we used for the explanation of mass spectral deconvolution is downloadable from here. Download
LC-MS/MS data set (.abf, non-labeled and fully 13C labeled Arabidopsis thaliana root samples) for computational metabolomics using stable isotope labeled organisms. Download
LC-MS/MS data set for all ion fragmentation with multiple collision energies. Download
LC-Ion mobility tandem MS (PASEF) data set for mouse tissues. Download (16 GB)
LC-MS/MS data set for mouse tissues. Download (5 GB)

MSDIAL metabolomics MSP spectral kit containing EI-MS, MS/MS, and CCS values (Last edited in Jan.10th, 2019)

MS/MS
All publicly available MS/MS records: Download (Positive, 72390 records), Download (Negative 32263 records)

MassBank Positive (8068 records) Download.
MassBank Negative (4782 records) Download.
MassBank-EU Positive (710 records) Download.
MassBank-EU Negative (100 records) Download.
ReSpect Positive (2737 records) Download.
ReSpect Negative (1573 records) Download.
GNPS Positive (8782 records) Download.
GNPS Negative (2351 records) Download.
Fiehn HILIC Positive (1701 records) Download.
Fiehn HILIC Negative (1341 records) Download.
CASMI2016 Positive (440 records) Download.
CASMI2016 Negative (178 records) Download.
MetaboBASE Positive (8 records) Download.
MetaboBASE Negative (1151 records) Download.
RIKEN PlaSMA authentic standards Positive (4439 records) Download.
RIKEN PlaSMA authentic standards Negative (4216 records) Download.
RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4) from plant tissues Positive (2384 records) Download.
RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4) from plant tissues Negative (1732 records) Download.
RIKEN oxidized phospholipids Negative (386 records) Download.
Karolinska institute and Gunma (GIAR) zic-HILIC deconvoluted MS2 spectra in data independent acquisition (814 records) Download.
Fiehn Pathogen Box Positive (392 records) Download.
Fiehn/Vaniya natural product library Positive (28347 records) Download.
Fiehn/Vaniya natural product library Negative (11590 records) Download.

EI-MS
All records with Kovats RI (15,302 records) Download.

Fiehn BinBase DB (Rtx5-Sil MS, predicted Kovats RI, 1021 records) Download.
RIKEN DB (Rtx5-Sil MS, Kovats RI, 241 records) Download.
Kazusa DB (Rtx5-Sil MS, Kovats RI, 273 records) Download.
GL-Science DB (InertCap 5MS-NP, Kovats RI, 494 records) Download.
Osaka Univ. DB (CPSil-8CB, Kovats RI, 430 records) Download.

All records with Fiehn RI (15,302 records) Download.

Fiehn BinBase DB (Rtx5-Sil MS, FAMEs RI, 1021 records) Download.
RIKEN DB (Rtx5-Sil MS, predicted Fiehn RI, 241 records) Download.
Kazusa DB (Rtx5-Sil MS, predicted Fiehn RI, 273 records) Download.
GL-Science DB (InertCap 5MS-NP, predicted Fiehn RI, 494 records) Download.
Osaka Univ. DB (CPSil-8CB, predicted Fiehn RI, 430 records) Download.

LipidBlast fork (Last edited in January 2th, 2020)

Currently, MS-DIAL internally has in silico MS/MS spectra for lipid identifications. Below is the LipidBlast (fork) templates that MS-DIAL partially uses.
Binary file (lbm2) for MS-DIAL lipidomics (ajusted Oliver Fiehn lab LC-MS method): Download
Binary file (lbm2) for MS-DIAL lipidomics (ajusted Makoto Arita lab LC-MS method): Download
Binary file (lbm2) for MS-DIAL lipidomics (ajusted Kazuki Saito lab LC-MS method): Download
ASCII file (lbm) for MS-DIAL lipidomics (ajusted Oliver Fiehn lab LC-MS method): Download
LipidBlast template for glycerolipids.
LipidBlast template for sphingolipids.
These libraries are also available as MSP format: Positive (32 class, 110,833 molecules, 143,342 spectra) and Negative (48 class, 154,770 molecules, 342,454 spectra).
The original LipidBlast is available from here.
The nomenclature for lipid classes in MS-DIAL lipidomics is shown at 'Lipid nomenclature in MS-DIAL lipidomics'.

Programs supporting MS-DIAL output

GNPS FBMN : The feature-based molecular networking (FBMN) supports the result of MS-DIAL by using "GNPS export" in alignment result export window.
MetFamily : This is designed for the identification and classification of regulated metabolite families by MS1 features and MS/MS.
LipidMatch : This supports rule based lipid identifications by means of MS/MS library.

Acknowledgement

This project was originally supported by NSF-JST Strategic International Collaborative Research Program (SICORP) for JP-US Metabolomics.
The current MS-DIAL program is maintained by RIKEN.

Lead developer: Hiroshi Tsugawa (RIKEN)
Current main developers: Hiroshi Tsugawa (RIKEN), Ipputa Tada (SOKENDAI), and Yuki Matsuzawa (RIKEN)
Main contributor: Diego Pedrosa (UC Davis) and Tomas Cajka (Czech Academy of Sciences)
Other supporters: Haruki Uchino (Keio Univ.) and Gert Wohlgemuth (UC Davis)
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