Program download

Main program is available from here. MS-FINDER program
MS-FINDER tutorial is available at MS-FINDER tutorial
The tutorial for MS-FINDER console application is written in this page.
MS-FINDER demonstration files. MS-FINDER demo files
The core source code of MS-FINDER is available from here. Download

Data templates available as MS-FINDER's input

MSP format as query file. Template
MAT format as query file. Template.
MAT format file including elements-fix information (the same format is used in MSP). Template
User defined structure library. Template.
Retention time library (InChIKey and RT pairs). Template.
CCS library (InChIKey, Adduct, and CCS pairs). Template.
Retention time and structure data for retention time prediction. Template.


MS-FINDER was launched as a universal program for compound ‘annotation’ that supports EI-MS (GC/MS) and MS/MS spectral mining. First, MS-FINDER aims to provide solutions for 1) formula predictions, 2) fragment annotations, and 3) structure elucidations by means of unknown spectra. In addition, the program can annotate your unknowns by the public spectral databases such as MassBank, LipidBlast, and GNPS.

Please cite

  • Hydrogen rearrangement rules: computational MS/MS fragmentation and structure elucidation using MS-FINDER software. Analytical Chemistry, 88, 7946-7958, 2016 [ACS page]
  • Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods, 15, 53-56, 2018 [NPG link]


This project was mainly supported by NSF-JST Strategic International Collaborative Research Program (SICORP) for JP-US Metabolomics.
MS-FINDER was developed between UC Davis Prof. Oliver Fiehn team and RIKEN CSRS (and NIG) Prof. Masanori Arita team.

Overview of MS-FINDER software

Graphical user interface of MS-FINDER is optimized for checking the annotation result of unknown spectra. The user can easily confirm the result of formula predictions with their isotopic ratio, product ion- or neutral loss matching, and database matching results. In addition, the result of structure elucidations can be found with their fragment detail, structure, and meta data.

Quick start MS-FINDER program via demo files

1. File import via a folder containing MSP or MAT (improved MSP) files

1'. File import via MS-FINDER GUI

1''. File import from MS-DIAL program

2. Parameter setting(see tutorial for the detail)

3. Formula predictions

4. Structure elucidations

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