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?
Thank you in advance!!
https://xcmsonline.scripps.edu/docs/fileformats.html Doesn't seem like xcms online likes compressed files.
I had previously seen the list you have linked, and I tried uploading the .d files unzipped, but they wouldn't load (they are .d file folders not a single file). When you enter the upload window the top specifically says: "select only .mzXML, .mzData, mzData.XML, mzML, .netcdf, .cdf, .d.zip, .wiff/.wiff.scan files"
Any thoughts?
No idea. I think you will have better luck contacting the xcms online people directly (https://xcmsonline.scripps.edu/landing_page.php?pgcontent=contact). They don't seem to frequent these waters unfortunately.