MS-FINDER statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool MS-FINDER

Tool usage distribution map

This map represents all the scientific publications referring to MS-FINDER per scientific context
info info

Associated diseases

This word cloud represents MS-FINDER usage per disease context

Popular tool citations

chevron_left Metabolite identification chevron_right
Want to access the full stats & trends on this tool?


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

[…] s 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 the further iden […]


Serum profile changes in postpartum women with a history of childhood maltreatment: a combined metabolite and lipid fingerprinting study

Sci Rep
PMCID: 5823924
PMID: 29472571
DOI: 10.1038/s41598-018-21763-6

[…] runs at fixed collision energies (10, 20, 40 V) against in-built MS/MS reference library LipidBlast. In addition, selected metabolite fragmentation information was directly exported from MS-DIAL into MS-Finder (version 2.10) for further spectra comparison. MS-FINDER predicts molecular formulas based on MS information and retrieves isomer structures from metabolome databases (including HMDB, PubChe […]


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
call_split See protocol

[…] were 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, v […]


Enhanced Isotopic Ratio Outlier Analysis (IROA) Peak Detection and Identification with Ultra High Resolution GC Orbitrap/MS: Potential Application for Investigation of Model Organism Metabolomes

PMCID: 5875999
PMID: 29346327
DOI: 10.3390/metabo8010009

[…] for metabolite identification are the in silico fragmentation methodologies []. In silico fragmentation software packages developed for prediction of ESI MS/MS spectra include CFM-ID [], MassFrag [], MS-Finder [], and Mass Frontier []. Blaženović et al. tested four different in silico fragmentation software packages for the Critical Assessment of Small Molecule Identification (CASMI) data analysis […]


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
call_split See protocol

[…] criterion of absolute intensity threshold 5 · 104 cps.Once LC-MS/MS data were acquired in a separate analytical run, molecular formulas were generated with the aid of SIRIUS 3.2 plus CSI:FingerID and MS-Finder tools. Few possible molecular structures with relatively high statistical scores were proposed per each molecular formula and searched in biological databases (ChEBI, HMDB, KEGG, KNApSAcK, M […]


Navigating freely available software tools for metabolomics analysis

PMCID: 5550549
PMID: 28890673
DOI: 10.1007/s11306-017-1242-7

[…] egories directly compare tools small molecule identification. In 2016 the categories were split into in silico fragmentation only and tools used along with additional information e.g. retention time. MS-FINDER (Tsugawa et al. ) and CFM-ID (Allen et al. ) were used by the teams who came 1st and 2nd respectively in the Full Information category and IOKR (Brouard et al. ) and fingerID (Heinonen et al […]

Want to access the full list of citations?
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.

MS-FINDER reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MS-FINDER