MS-DIAL

Program download

Main program is available from here. MS-DIAL program
MS-DIAL tutorial is downloadable from here. MS-DIAL tutorial
The tutorial for MS-DIAL console application is written in this page
File converter is downloadable from here. File converter
FAQ for MS-DIAL and ABF file converter.
MS-DIAL mathematics is downloadable from here. MS-DIAL mathematics
Nomenclature in MS-DIAL lipidomics is described here.
The core source code of MS-DIAL is available from here. 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

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

  • MS-DIAL: data independent MS/MS deconvolution for comprehensive metabolome analysis. Nature Methods, 12, 523-526, 2015 [PubMed]
  • Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods, 15, 53-56, 2018 [NPG link]

FAQ

See FAQ web page too, for the usage of MS-DIAL and ABF file converter.

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. data independent acquisition (SWATH) and data dependent acquisition (IDA) for algae lipidomics; 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. data dependent acquisition for Wine metabolome;
GC-MS data set (.cdf and .abf files) for small biomolecule analysis of Arabidopsis thaliana and Alage is available from here. GC/MS data set;
HILIC-SWATH-MS data (.wiff, .wiff.scan, and .abf) that we used for the explanation of mass spectral deconvolution is downloadable from here. HILIC(+)-SWATH-MS
LC-MS/MS data set (.abf, non-labeled and fully 13C labeled Arabidopsis thaliana root samples) for the determination of carbon element count for metabolite annotation. Data set of Nonlabeled- and fully 13C labeled plant tissues;
LC-MS/MS data set for all ion fragmentation with multiple collision energies. DIA-MS with multiple CEs

Curated spectra download (MSP format: Last edited in Oct.12, 2018)

MS/MS
All publicly available MS/MS records: Positive (29,269 records), Negative (17,810 records)

MassBank Positive (8068 records) MassBank (Positive).
MassBank Negative (4782 records) MassBank (Negative).
MassBank-EU Positive (710 records) MassBank-EU (Positive).
MassBank-EU Negative (100 records) MassBank-EU (Negative).
ReSpect Positive (2737 records) ReSpect (Positive).
ReSpect Negative (1573 records) ReSpect (Negative).
GNPS Positive (8782 records) GNPS (Positive).
GNPS Negative (2351 records) GNPS (Negative).
Fiehn HILIC Positive (1701 records) Fiehn-HILIC (Positive).
Fiehn HILIC Negative (1341 records) Fiehn-HILIC (Negative).
CASMI2016 Positive (440 records) CASMI2016 (Positive).
CASMI2016 Negative (178 records) CASMI2016 (Negative).
MetaboBASE Positive (8 records) MetaboBASE (Positive).
MetaboBASE Negative (1151 records) MetaboBASE (Negative).
RIKEN PlaSMA authentic standards Positive (4439 records) RIKEN PlaSMA authentic standards Positive (Positive).
RIKEN PlaSMA authentic standards Negative (4216 records) RIKEN PlaSMA authentic standards Positive (Negative).
RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4) from plant tissues Positive (2384 records) RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4) from plant tissues (Positive).
RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4) from plant tissues Negative (1732 records) RIKEN PlaSMA bio-MS/MS (MSI level 1,2,3, or 4) from plant tissues (Negative).
RIKEN oxidized phospholipids Negative (386 records) RIKEN oxidized phospholipids (Negative).

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

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

All records with Fiehn RI (15,302 records) All of public records.

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

LipidBlast fork (Last edited in Oct.1, 2018)

Currently, MS-DIAL internally has in silico MS/MS spectra for lipid identifications. Below is the LipidBlast (fork) templates that MS-DIAL partially uses.
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'.

Related programs supporting MS-DIAL output

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 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) and Ipputa Tada (SOKENDAI)
Main contributor: Diego Pedrosa and Tomas Cajka (UC Davis)
Other supporters: Haruki Uchino (RIKEN, Keio Univ.) and Gert Wohlgemuth (UC Davis)

How to use See MS-DIAL tutorial for the detail

1. Convert vendor's format file into ABF format file
MS-DIAL imports our common data format (ABF). The file converter can be freely downloaded from Download
Currently, all of major MS vendor's format as well as common data format such as mzML and netCDF is supported.

2. Start up of a MS-DIAL project
MS-DIAL provides the data processing solution for all type of data sets including GC/MS, data dependent/independent acquisition, positive/negative ion mode, and metabolomics/lipidomics application. In the start up window, users can choose (A) project type: GC/MS or LC/MS, (B) data type: centroid or profile, (C) ion mode: positive or negative, and (D) omics type: metabolomics or lipidomics.

3. Parameter settings
Some parameters should be determined for data collection, peak detection, de-convolution, identification, and alignment. See the tutorial and mathematics for the detail. As the starter kit, you can utilize the above NIST MSP DBs. Also, the lipid identification is now straightforward since MS-DIAL internally has in silico retention time and MS/MS spectra of major lipid species.

4. Main window (data curation, normalization, statistical analysis and export)
Graphical user interface of MS-DIAL is optimized for metabolomics and lipidomics. The user can easily confirm the identification or peak alignment result and manually curate the identification result.

Futher statistics

MS-DIAL supports interpolation methods for missing values, normalization methods (internal standard, LOESS/Cubic-spline etc.), and principal component analysis.
Moreover, we also provide a tool for statistics by microsoft excel at excel macro based statistical analysis tool page.

Source code data processing, cheminformatics, and database

The main source code is available from here. MS2Dec sample program.
The demo file (mzML: HILIC-LC/SWATH/MS for a human plasma) and an Analyst experiment file (25-Da setting) are downloadable from here. MS2Dec sample program demo file.

This program is for one mzML file of SWATH-MS exported by ProteoWizard (64 bit and profile mode).
This program exports the peak detection and deconvolution result, i.e. retention time, precursor m/z, abundance, raw MS/MS spectrum, and deconvoluted MS/MS spectrum.
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