MS-DIAL
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
General and plant metabolomics: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods, 16, 295–298, 2019 [NPG link]
GC-MS project: Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods, 15, 53–56, 2018 [NPG link]
DIA-MS and Lipidomics: MS-DIAL: data independent MS/MS deconvolution for comprehensive metabolome analysis. Nature Methods, 12, 523–526, 2015 [PubMed]
Software
MS-DIAL
Latest version
Download
Repository
Old versions
Link
Core
Souce code
Download
Library
Templates
.txt files
Link in page
Demonstration
.abf files etc.
Link in page
Curated MSP spectral library
.msp files
Link in page
Tutorial
Tutorial
mtbinfo-team.github.io
Link
AIF data processing
and spectral library construction methodology
Tutorials and parameter files
Download
Console App
Terminal operation page
Link
Forum & FAQ
Forum
www.metabolomics-forum.com
Link
MS-DIAL
ABF file converter
FAQ page
Link
Mathematics
.pdf file
Download
Related page
Compound identification
and annotation confidence
Annotation 'code' page
Link
Lipid nomenclature
Nomenclature page
Link
ABF file converter
www.reifycs.com
Link
Library templates
See below for MSP format files.
Text format library for metabolite identifications.
SWATH-MS experiment file.
All-ions experiment file (MSE, all-ions, all ion fragmentations etc).
Multiple CEs all-ions experiment file.
Reference library for diagnostic marker ions for retention time correction in LC-MS projects.
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).
Text format library for metabolite identifications using CCS. MS/MS Positive.
Text format library for metabolite identifications using CCS. MS/MS Negative.
(For CCS resources, see AllCCS database and PNNL CCS database).
Demonstration files
Lipid profiling of algae.
LC-MS/MS Dataset
.wiff
.wiff.scan
.abf
Hydrophilic metabolome profiling of Wine.
(data dependent MS/MS acquisition.)
LC-MS/MS Dataset
.abf
Small biomolecule analysis of Arabidopsis thaliana and Alage.
GC-MS Dataset
.cdf
.abf
That we used for the explanation of mass spectral deconvolution.
HILIC-SWATH-MS Data
.wiff
.wiff.scan
.abf
Computational metabolomics using stable isotope labeled organisms.
(non-labeled and fully 13C labeled Arabidopsis thaliana root samples.)
LC-MS/MS Dataset
.abf
All ion fragmentation with multiple collision energies.
LC-MS/MS Dataset
.abf
Mouse tissues.(15.8GB)
LC-Ion mobility tandem MS (PASEF) Dataset
.ibf
RAW
Mouse tissues.(3.6GB)
LC-MS/MS Dataset
.wiff
.wiff.scan
.abf
MS-DIAL metabolomics MSP spectral kit
containing EI-MS, MS/MS, and CCS values
Last edited in Jan.10th, 2019.
All publicly available MS/MS
MS/MS Positive
72,390
records
All publicly available MS/MS
MS/MS Negative
32,263
records

MassBank
MS/MS Positive
8,068
records
MassBank
MS/MS Negative
4,782
records
MassBank-EU
MS/MS Positive
701
records
MassBank-EU
MS/MS Negative
100
records
ReSpect
MS/MS Positive
2,737
records
ReSpect
MS/MS Negative
1,573
records
GNPS
MS/MS Positive
8,782
records
GNPS
MS/MS Negative
2,351
records
Fiehn HILIC
MS/MS Positive
1,701
records
Fiehn HILIC
MS/MS Negative
1,341
records
CASMI2016
MS/MS Positive
440
records
CASMI2016
MS/MS Negative
178
records
MetaboBASE
MS/MS Positive
8
records
MetaboBASE
MS/MS Negative
1,151
records
RIKEN PlaSMA authentic standards
MS/MS Positive
4,439
records
RIKEN PlaSMA authentic standards
MS/MS Negative
4,216
records
RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4)
from plant tissues
MS/MS Positive
2,384
records
RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4)
from plant tissues
MS/MS Negative
1,732
records
Karolinska institute
and Gunma (GIAR) zic-HILIC deconvoluted MS2 spectra
in data independent acquisition
MS/MS Positive
814
records
Fiehn Pathogen Box
MS/MS Positive
392
records
Fiehn/Vaniya natural product library
MS/MS Positive
28,347
records
Fiehn/Vaniya natural product library
MS/MS Negative
11,590
records

All records with Kovats RI
EI-MS
15,302
records

Fiehn BinBase DB (Rtx5-Sil MS, predicted Kovats RI)
EI-MS
1,021
records
RIKEN DB (Rtx5-Sil MS, Kovats RI)
EI-MS
241
records
Kazusa DB (Rtx5-Sil MS, Kovats RI)
EI-MS
273
records
GL-Science DB (InertCap 5MS-NP, Kovats RI)
EI-MS
494
records
Osaka Univ. DB (CPSil-8CB, Kovats RI)
EI-MS
430
records

All records with Fiehn RI
EI-MS
15,302
records

Fiehn BinBase DB (Rtx5-Sil MS, FAMEs RI)
EI-MS
1,021
records
RIKEN DB (Rtx5-Sil MS, predicted Fiehn RI)
EI-MS
241
records
Kazusa DB (Rtx5-Sil MS, predicted Fiehn RI)
EI-MS
273
records
GL-Science DB (InertCap 5MS-NP, predicted Fiehn RI)
EI-MS
494
records
Osaka Univ. DB (CPSil-8CB, predicted Fiehn RI)
EI-MS
430
records
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.
The nomenclature for lipid classes in MS-DIAL lipidomics is shown at 'Lipid nomenclature in MS-DIAL lipidomics'.
MS-DIAL lipidomics (adjusted Oliver Fiehn lab LC-MS method)
.ibm2
MS-DIAL lipidomics (adjusted Makoto Arita lab LC-MS method)
.ibm2
MS-DIAL lipidomics (adjusted Kazuki Saito lab LC-MS method)
.ibm2
MS-DIAL lipidomics (adjusted Oliver Fiehn lab LC-MS method)
.ibm
LipidBlast template for glycerolipids
.xlsx
LipidBlast template for sphingolipids
.xlsx
These libraries are also available as MSP format.
Positive (32 class, 110,833 molecules, 143,342 spectra)
.msp
These libraries are also available as MSP format.
Negative (48 class, 154,770 molecules, 342,454 spectra)
.msp
Programs supporting MS-DIAL output
The feature-based molecular networking (FBMN) supports the result of MS-DIAL
by using "GNPS export" in alignment result export window.
This is designed for the identification and classification of regulated metabolite families
by MS1 features and MS/MS.
This supports rule based lipid identifications
by means of MS/MS library.
Acknowledgement
This project was supported
by NSF-JST Strategic International Collaborative Research Program (SICORP) for JP-US Metabolomics.
MS-DIAL is mainly developed between UC Davis Prof.
Oliver Fiehn team and RIKEN CSRS (and NIG) Prof. Masanori Arita team.
Lead developer
Hiroshi Tsugawa
RIKEN
Current main developers
Hiroshi Tsugawa
RIKEN
Current main developers
Yuki Matsuzawa
RIKEN
Current main developers
Ipputa Tada
SOKENDAI
Current main developers
Mikiko Takahashi
RIKEN
Main contributors
Diego Pedrosa
UC Davis
Main contributors
Tomas Cajka
UC Davis
Other supporters
Haruki Uchino
RIKEN, Keio Univ.
Other supporters
Gert Wohlgemuth
UC Davis
RIKEN
CSRS
PRIMe
RIKEN Center for Sustainable Resource Science : Metabolome Informatics Research Team
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
Creative Commons License