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Citations per year

Number of citations per year for the bioinformatics software tool TargetSearch
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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

Information


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
Requirements
methods, R(>=2.7.0), tcltk, xcms, TargetSearchData
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Matthew A. Hannah

Publication for TargetSearch

TargetSearch citations

 (8)
library_books

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

2017
GigaScience
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 […]

library_books

VMP1 deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesis

2014
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 […]

library_books

Computational mass spectrometry for small molecules

2013
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 […]

library_books

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

2012
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 […]

library_books

A distinct metabolic signature predicts development of fasting plasma glucose

2012
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 […]

library_books

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

2010
PLoS One
PMCID: 2990718
PMID: 21124901
DOI: 10.1371/journal.pone.0014101

[…] .leco.com). 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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