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FingerID specifications


Unique identifier OMICS_04649
Name FingerID
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Markus Heinonen

Publication for FingerID

FingerID citations


Navigating freely available software tools for metabolomics analysis

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

[…] ct MS/MS spectra at three collision energies: 10 V, 20 V and 40 V. MS/MS spectra can be searched against the HMDB (Wishart et al. ) or KEGG databases (Kanehisa et al. ) for metabolite identification. FingerID (Heinonen et al. ) uses kernel methods to predict a large set of molecular properties for MS/MS matching, searching the PubChem (Kim et al. ), MassBank (Horai et al. ) and METLIN (Smith et al […]


Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

J Cheminform
PMCID: 5445034
DOI: 10.1186/s13321-017-0219-x

[…] sed to identify MS/MS spectra when the reference MS/MS spectrum is not available. Such software tools include MetFrag [], MIDAS [], MAGMa [, ], MAGMa+ [], MOLGEN–MS/MS [], CSI:FingerID [], CFM-ID [], FingerID [], Input output kernel regression (IOKR) [] and the MS-Finder software []. A number of commercial software solutions such as MassFrontier (HighChem), MS-Fragmenter (ACD/Labs) or Molecular St […]


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

[…] hierarchical trees of predicted substructures capable of explaining MSn data, where each level takes into account the restrictions imposed by the assignment of precursor and subsequent fragmentation. FingerId [] developed a model based on a large dataset of tandem MS from MassBank and uses a support vector machine to predict the molecular fingerprint of the unknown spectra and compare this with th […]


FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry

Sci Rep
PMCID: 5430893
PMID: 28455528
DOI: 10.1038/s41598-017-01390-3

[…] CFM-ID, FingerID and MetFrag, which are well-known metabolite prediction tools that use different prediction models, were used for the comparison. The settings for these tools are shown in Supplementary Table […]


Fast metabolite identification with Input Output Kernel Regression

PMCID: 4908330
PMID: 27307628
DOI: 10.1093/bioinformatics/btw246

[…] We compared the performances of our method with two competing methods: FingerID () and CSI:FingerID. showed that CSI:FingerID improved significantly the metabolite identification rate compared with competing methods including CFM-ID (), MetFrag (), MAGMa (), MIDAS () as […]


MetFrag relaunched: incorporating strategies beyond in silico fragmentation

J Cheminform
PMCID: 4732001
PMID: 26834843
DOI: 10.1186/s13321-016-0115-9

[…] to those here, their results on the Agilent dataset indicated that MetFrag2010 and CFM-ID achieved 9 and 12 % top 1 (expected) ranks, which are reasonably comparable with the results presented above. FingerID [] achieved 19.6 %, while CSI:FingerID achieved 39 % top 1 results, which is a dramatic improvement over the other fragmenters. Since the external information boosted the top 1 ranks to 73 % […]


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FingerID institution(s)
Department of Computer Science, University of Helsinki, Helsinki, Finland

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