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For peak alignment, only the (recommended) option of the "fast aligner" was tested as the other alignment procedure resulted in frequent crashes of the computer.
Although we believe the strategy of correcting for peak fragment lengths before peak alignment can increase the accuracy of peak alignment and make visual evaluation of aligned peak sets easier, some researchers might not agree.
PyMS[238] comprises several functions for processing raw GC-MS data, such as noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment.
The peak finding, peak alignment, and peak filtering of ESI+ raw data were carried out with MarkerLynx applications manager version 4.1 (Waters).
Furthermore, mass data were exported to ProfileAnalysis 1.1 software (Bruker), which allowed for peak alignment, background noise subtraction and data reduction.
A MATLAB implementation of the software package, called WaveSpect0, is presented including processing procedures of step-interval unification, adaptive stationary discrete wavelet denoising, baseline correction using splines, normalization, peak detection, and a newly designed peak alignment method using clustering techniques.
The GC-FID data analyses was based on automatic peak alignment and integration, enabling extraction of the area of 140 peaks from the gas chromatograms, as opposed to the 31 fatty acids usually considered for fish oil characterisation.
After gas chromatography mass spectrometry (GC MS) analysis, data processing, including retention time correction, spectral deconvolution, peak alignment, and normalization prior to statistical analysis, is an important step in metabolomics.
Recently, a number of software that can be downloaded from websites are available [15]; for example, "DrDmassPlus" ([75], http://kanaya.naist.jp/DrDMASSplus/) can be used to treat metabolome data from FT-ICR MS, including the functions of peak picking, peak alignment, and some statistical analyses.
SpecAlign [ 134] was used for peak alignment of the spectra.
Peak alignment and detection were performed according to manufacturer protocols.
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