There are two possible reasons when this error happens:
The zip files cannot be decompressed by our program. This happens if you used the most recent WinZip (v12.0) with default option for compression. Make sure to selecting the Legacy compression (Zip 2.0 compatible).
It can also be caused by the spectra itself. They must be in the formats accepted by MetaboAnalyst (mzML, mzXML, netCDF, etc) . Also, please note, the program does not handle tandem-MS files. In addition, make sure there are no other files (for example, log file or other parameters files) included in the spectra folder.