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Popular tool citations

chevron_left Metabolite identification Spectral deconvolution Chromatogram alignment Metabolite identification Peak detection Noise filtering Spectral visualization Peak detection Spectral visualization Spectral deconvolution Peak alignment chevron_right
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TargetSearch specifications


Unique identifier OMICS_09688
Name TargetSearch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2.0
Stability Stable
methods, R(>=2.7.0), tcltk, xcms, TargetSearchData
Maintained Yes


No version available



  • person_outline Matthew A. Hannah

Publication for TargetSearch

TargetSearch citations


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

[…] de an interactive user interface facilitating use by unexperienced users. They do, however, require several manual input and data check steps that are time consuming and negate truly high throughput. TargetSearch [] uses similar approaches to process data and identify and quantify targeted metabolites based on retention time index and spectra-matching of multiple correlated masses, but they are hi […]


VMP1 deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesis

BMC Plant Biol
PMCID: 4108031
PMID: 24885763
DOI: 10.1186/1471-2229-14-121

[…] and mass spectrometry (GC-MS) analysis was performed as described []. Briefly: six biological replicates from each strain were subjected to GC-MS analysis. Metabolite levels were determined using the TargetSearch software package []. The metabolites' retention indexes (+/−2 s) and spectra (similarity > 85%) were compared against compounds stored in the Golm Metabolome Database (GMD []). Secondary […]


Computational mass spectrometry for small molecules

J Cheminform
PMCID: 3648359
PMID: 23453222
DOI: 10.1186/1758-2946-5-12

[…] he quantitative analysis of GC-MS-based metabolite profiling experiments. The MetaboliteDetector[] detects and subsequently identifies metabolites and allows for the analysis of high-throughput data. TargetSearch[] iteratively corrects and updates retention time indices for searching and identifying metabolites. Metab[] is an R package that automates the pipeline for analysis of metabolomics GC-MS […]


Metabolic Profiling Reveals Sphingosine 1 Phosphate Kinase 2 and Lyase as Key Targets of (Phyto ) Estrogen Action in the Breast Cancer Cell Line MCF 7 and Not in MCF 12A

PLoS One
PMCID: 3480432
PMID: 23112854
DOI: 10.1371/journal.pone.0047833

[…] rpm, 4°C, 2 min). Sample extraction and derivatization followed the procedure described previously . Metabolite signals were obtained from raw data and compared against a reference database using the TargetSearch package . Some samples were removed after inspection of their chromatograms due to overall lower peak intensities, leaving four to six replicates per group (all samples of the same genoty […]


A distinct metabolic signature predicts development of fasting plasma glucose

J Clin Bioinforma
PMCID: 3298809
PMID: 22300499
DOI: 10.1186/2043-9113-2-3

[…] classes, such as amino acids, carbohydrates, organic acids, fatty acids and steroids.The chromatographic peaks were picked and identified using the Golm Metabolome Database (GMD) [] and the R package TargetSearch []. Since missing values only occurred if metabolite concentration went below detection limit, these values were replaced by a value 0.7 times the minimum measured value. Log-transformati […]


Interaction with Diurnal and Circadian Regulation Results in Dynamic Metabolic and Transcriptional Changes during Cold Acclimation in Arabidopsis

PLoS One
PMCID: 2990718
PMID: 21124901
DOI: 10.1371/journal.pone.0014101

[…] Chromatogram acquisition parameters used were as described . Chromatograms were exported from Leco ChromaTOF software (version 3.25) to R software. Metabolite data were analyzed using the TargetSearch package . Data were normalized by dividing each metabolite value by the median of all values for this metabolite measured in the same batch followed by a normalization to the sample media […]

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TargetSearch institution(s)
Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany; Centro de Biotecnología, Universidad Técnica Federico Santa María, Chile; RIKEN Plant Science Center, Tsurumi-ku, Suehiro-cho, Kanagawa, Japan; Bayer BioScience N.V., Technologiepark 38, Gent, Belgium

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