TargetSearch

Version: 1.2.0

Website

http://bioconductor.org/packages/2.5/bioc/html/TargetSearch.html

Description

This Bioconductor packages provides both preprocessing and metabolite identification of GC-MS data: providing peak picking, RT alignment and metabolite identification via libraries. Features are picked using peak apex intensities rather than deconvolution as deconvolution can induce errors resulting in mixed mass spectral tags (MSTs). As input it requires raw data in the netCDF format (ideally pre-baseline corrected), a text file of metadata and a reference library of MSTs. For RT correction to be performed a tab separated file of retention time index (RI) markers must be provided. If baseline correction was not performed using the vendor software, this functionality is provided in TargetSearch. After this, peak apex intensities are used for peak picking. Retention time alignment is then performed using the RI. Metabolites can then be identified by user inputed libraries.

Functionality

• Preprocessing

Instrument Data Type

• MS/GC-MS

Approaches

• Targeted

Computer Skills

Advanced

Software Type

Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R, C

Dependencies

R (≥ 2.7.0), mzR

Input Formats - Open

netCDF

Input Formats - Proprietary

N/A

Published

2009

Last Updated

2016

License

GPL (≥ 2)

Paper

http://www.ncbi.nlm.nih.gov/pubmed/20015393

PMID

20015393