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IDMass 2.0: Component Extraction, Identification and Statistics GUI Processing Toolkit for GC-MS
Date Issued
2014
Date
2014
Author(s)
Tan, Cheng-En
Abstract
Gas chromatography coupled with mass spectrometer (GC/MS) has become an important technique for metabolomics. There are some key steps including pre-processing, peak detection, deconvolution for GC/MS data analysis. Currently a number of accessible software are developed, however there are few software can provide both all necessary functions for GC/MS data analyses which are integrated into pipeline and result visualization. In the previous time, IDMass has been developed by us with an automatic pipeline integrated all necessary functions for GC-MS data analysis, and now we modified and improve IDMass 1.0 to become new IDMass 2.0. There are six additional features compare with IDMass 1.0. First, we add gap filling in chemical rank procedure. By comparing the results of chemical rank detection, this procedure can fill the chemical ranks which are not detected in only few samples. Second, we add component alignment procedure after component extraction. This procedure clusters the extracted components and all members in clusters will be identified as the same compound. At the same time, we modified the algorithm of component extraction procedure in IDMass 1.0 to reduce the computation time with the similar accuracy compare with previous version. In previous algorithm, both chromatogram and spectrum optimization were applied for each iterative loop, however there were too many possible combination of chromatograms and spectra to allow the program optimize them fast. We separate the procedures of optimization into two different optimization procedures to reduce the possible combination cases of chromatograms and spectra therefore reduce the computation time. The first two significances improve both computation speed and identification performance including true positive, false negative and false positive. Third, we provide graphical user interface (GUI) and provide compound-oriented viewing to allow users observe or compare the expression level in different experimental groups or all samples of specified compounds. Fourth, we design and implement novel method of chemical rank detection for GC/Q-MS data with low scan rate. Fifth, we integrate these additional procedures and improvements into automated pipeline in IDMass 1.0. Users can process all GC/MS data after setting all related parameters in GUI parameter settings window or parameter configuration files. Finally, we integrated GUI shell written in Python, R procedures and related packages into a software program. Users can use directly after installation with installer without any additional settings. All codes are written in R and Python and there are common platform on these two environment created by Rpy2 package. Users can add any Python or R packages to extend IDMass 2.0.
Subjects
Gas Chromatography coupled with mass spectrometer
gap filling in chemical rank
component alignment
component extraction
graphical user interface
platform-independent software
metabolomics
Type
thesis
File(s)
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Name
ntu-103-R01922031-1.pdf
Size
23.32 KB
Format
Adobe PDF
Checksum
(MD5):111e2c40774a373936675a43ccee59fb