I am very new to metabolomics and have previously been using metaboanalyst.com to process data files I have received from the metabolomics core at my facility. My PI and I were disappointed with the processing of metaboanalyst so I wanted to try XCMS instead. My samples were run on a 1200 Agilent UPLC connected to Q-ToF-MS (6550 Agilent). I requested the raw files from the core and they sent me .d folders. I zipped the folder for each sample individually (4 samples x 2 technical replicates = 8 .d.zip files for 2 different conditions) and then uploaded them to XCMS using the "paired job" option. Unfortunately it didn't work and I got these error messages: NO_VALID_DOT_D_FILE and FILE_CONVERSION_ERROR. Can anyone tell me what I may have done wrong?
