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MS-FINDER specifications


Unique identifier OMICS_24909
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data Some queries of MS and MS/MS spectra.
Input format MSP,MAT
Operating system Windows
Programming languages C#
Computer skills Medium
Version 2.24
Stability Stable
Maintained Yes




No version available



  • person_outline Oliver Fiehn
  • person_outline Masanori Arita
  • person_outline Hiroshi Tsugawa

Publication for MS-FINDER

MS-FINDER citations


Metabolic profiling of sourdough fermented wheat and rye bread

Sci Rep
PMCID: 5890289
PMID: 29632321
DOI: 10.1038/s41598-018-24149-w

[…] performed in ms-dial. for some of the compounds with no spectral database matches, tentative ids were given based on in silico generated ms/ms spectra acquired from molecular database entries using ms-finder software. for the identification of small peptides, fragment motifs specific for amino acid residues were determined from the identifications based on ms/ms data and used […]


In vivo validation of anti malarial activity of crude extracts of Terminalia macroptera, a Malian medicinal plant

Malar J
PMCID: 5800286
PMID: 29402267
DOI: 10.1186/s12936-018-2223-7

[…] processed with ms-dial v.2.56 for mass signal extraction and peaks alignment []. molecular formula prediction and compound annotation of significant features (m/z, rt pairs) were calculated with ms-finder 2.10 []. only natural product databases focused on plants were selected [i.e. universal natural products database (unpd), knapsac, plantcyc, dictionary of natural products (dnp, crc press, […]


Changes of Metabolomic Profile in Helianthus annuus under Exposure to Chromium(VI) Studied by capHPLC ESI QTOF MS and MS/MS

PMCID: 5735654
PMID: 29359067
DOI: 10.1155/2017/3568621

[…] of intensity threshold 5 · 104 cps, fold change ≥ 5, and p ≤ 0.01, yielding precursor ions. molecular formulas were assigned based on data processing with two computational tools (sirius and ms-finder); annotation of candidate structures was performed by database search using csi:fingerid and ms-finder. even though ultimate identification has not been achieved, it was demonstrated […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] it slightly slower than mfsearcher, but hr3 includes compounds with atoms that are not present in mfseacher's list, as well as considering matches to the isotopic pattern within its annotations. ms-finder [] is a c# program with a gui providing a constraint-based filtering method for selecting structure candidates. the workflow begins with molecular formulas from precursor ions […]


Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library

J Cheminform
PMCID: 5352698
PMID: 28316657
DOI: 10.1186/s13321-017-0205-3

[…] of sphingolipids. we created theoretical ms/ms spectra for 21 sphingolipid classes in human and mouse (109,448 molecules), with substructure-level annotation of unique fragment ions by ms-finder software. the existence of ceramides with β-hydroxy fatty acids was confirmed in mouse tissues based on cheminformatic- and quantum chemical evidences. the rt of sphingo- and glycerolipid […]

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MS-FINDER institution(s)
RIKEN Center for Sustainable Resource Science, Yokohama, Japan; Genome Center, University of California−Davis, Davis, CA, USA; Reifycs Inc., Tokyo, Japan; Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan; Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
MS-FINDER funding source(s)
Supported by the NSF-JST Strategic International Collaborative Research Program (SICORP) for JP-US Metabolomics; the Database Integration Coordination Program of the National Bioscience Database Center; Grant-in-Aid for Scientific Research on Innovative Areas 15H05897; the JSTCore Research for Evolutionary Science and Technology (JSTCREST); partially the Japan Advanced Plant Science Network, a grant-in-aid for scientific research (C) 15K01812, the corresponding Grant NSF MCB 1139644, and NSF CBET 1438211, NIH 2R01HL091357-05, and AHA 15SDG25760020, the P20 Program NIH HL113452 Grant supported by National Institutes of Health (NIH), Grant NIH DK097154 and the QTOFMS instrument through NIH Grant S10-RR031630.

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