For multivariate data analysis using metaboanalyst, first you've to arrange your data (processed though various software program e.g. Sieve, MarkerLynx; etc) in groups and save the file as CSV format. Then you can use this format file in metaboanalyst.
In the metaboanalyst home page there are some tutorials, you could also take help form the tutorial.
You could get more informations regarding metaboanalyst if you go through the following article...