MzXML

In a GC-MS or LC-MS metabonomics experiment each file represents a single biological sample. The basic goal of data processing is to transform raw data files to a standard and uniform format so that statistical analyses can be carried out. A variety of instrument vendors utilize different proprietary data formats. Thus, the first step in data processing requires a conversion of such raw proprietary data into common raw data format such as ASCII text or binary netCDF. More recently, a universal mzXML format has become more popular. Many vendor instrument software packages contain scripts to allow for such a file conversion [76],... 

The data must be converted from the Bruker ftd file format to the more general mzXML format. The CompassX-port software is run along with the - multiName tag at an MS-DOS prompt to create a file called new.mzXML within each spectrum directory. 

MATLAB is used along with the bioinformatics toolbox and the batch conversion wrapper code available online see Note 10) to convert mzXML files into spectra-containing text files. During this step, the data may be processed by baseline subtraction and smoothing with the Bioinformatics Toolbox functions in MATLAB to eliminate noise and create more uniform ion images. 

Agilent MS Engine Files mzXML/mzData Files NetCDF Files PerkinElmer Files Shimadzu MS Files Schrader/GCMate Files Varian MS Files Varian SMS Files Varian XMS Files Xcalibur Raw Files... 

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