A xar.xml can also be imported via the Process and Import Data
button on the Data Pipeline. Examples 4 and 5 in the tutorial
include references to MS2 data files. If these xar.xml files are loaded via the Data Pipeline and the file references are correct, the pipeline will automatically initiate an upload of the referenced MS2 data. This feature is not available on the Import Experiment
page mentioned here
The xar.xml experiment description document is not intended to contain all of the raw data and intermediate results produced by an experiment run. Experimental data are more appropriately stored and transferred in structured documents that are optimized for the specific data and (ideally) standardized across machines and software applications. For example, MS2 spectra results are commonly transferred in "mzXML" format. In these cases the xar.xml file would contain a relative file path to the mzXML file in the same directory or one of its subdirectories. To transfer an experiment with all of its supporting data, the plan is that the folder containing xar.xml and all of its subfolder contents would be zipped up into an Experment Archive file with a file extension of "xar". In this case the xar.xml file acts like a "manifest" of the archive contents, in addition to its role as an experiment description document.