CSI:FingerID statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CSI:FingerID

Tool usage distribution map

This map represents all the scientific publications referring to CSI:FingerID per scientific context
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CSI:FingerID specifications


Unique identifier OMICS_27267
Name CSI:FingerID
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.1.2
Stability Stable
Maintained Yes


  • person_outline Sebastian Bocker

Publications for CSI:FingerID

CSI:FingerID citations


American Gut: an Open Platform for Citizen Science Microbiome Research

PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] tion in reference (). In addition, commendamide and its analog were identified by matching the exact mass of the corresponding ion and by in silico prediction of the MS/MS fragmentation spectra with CSI:FingerID () (). For novel molecules that were found within the cluster of compounds of interest but were not described in the literature previously, the structure was postulated using annotation p […]


Discovery of urinary biomarkers to discriminate between exogenous and semi endogenous thiouracil in cattle: A parallel like randomized design

PLoS One
PMCID: 5896977
PMID: 29649241
DOI: 10.1371/journal.pone.0195351

[…] ragmentation spectrum (allowed deviations for in silico fragment matching ≤ 60 ppm or 0.02 Da). Data interpretation was supported by XCalibur 3.0 (Thermo Fisher Scientific, San Jose, USA), MZmine [], CSI:FingerID [], MetFrag [], MAGMa, and MZCloud.For a first set of compounds (, ), a strong structural relationship was noted between the proposed tentative identities and TU, which of course strongly […]


Promising Metabolite Profiles in the Plasma and CSF of Early Clinical Parkinson's Disease

PMCID: 5844983
PMID: 29556190
DOI: 10.3389/fnagi.2018.00051

[…] e databases such as Metlin and MassBank (validation level 2) or against in silico fragmentation spectra (validation level 3) retrieved from Metfrag (Ruttkies et al., ), CFM-ID (Allen et al., ) and/or CSI:FingerID (Dührkop et al., ) with precursor mass accuracy of 20 ppm and fragment accuracy of 0.01 Da. Semi-quantitative metabolite intensities were calculated using the raw peak height. […]


Beyond genomics: understanding exposotypes through metabolomics

Hum Genomics
PMCID: 5787293
PMID: 29373992
DOI: 10.1186/s40246-018-0134-x

[…] lite can be represented as multiple signals []. Tools such as CAMERA [], RAMClust [], and “Credentialing” [] have helped overcome this problem and improve peak annotation. Other notable tools include CSI:FingerID [] which predicts the fragmentation of metabolites using an in silico method, thus aiding in metabolite identification, and “integrated-omics” housed on XCMSOnline [] (http://xcmsonline.s […]


Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

PMCID: 5875998
PMID: 29342073
DOI: 10.3390/metabo8010008

[…] ention in recent years. There are multiple publicly available software and web servers allowing the query of experimental LC-MS and LC-MS/MS data for identification of unknowns, including MetFrag and CSI:FingerID [,,].The second strategy, on the other hand, relies on the NMR technique, in which the experimental chemical shifts of unknown metabolites are sequentially assigned and deconvoluted by mu […]


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

[…] approaches under 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, […]

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CSI:FingerID institution(s)
Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
CSI:FingerID funding source(s)
Supported by the Deutsche Forschungsgemeinschaft [BO 1910/20-1].

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