TSEM extracts signals from a LCMS data file for a given list of target compounds.
1) Organize raw data files by chromatography types ("RP" and "HILIC") and ESI modes ("ESIPOS" and "ESINEG").
2) Convert raw data to mzML format using the MSConvert (proteowizard) software.
3) Create a folder "IDSL" in your Google Drive, and create a sub-directory "LCMS" in it.
4) Create a folder for the study in "LCMS" folder, and upload the mzML files to corresponding sub-folders from #1.
5) Upload the target list in each folder. The target file (.xlsx) must include three columns 1) compound_name 2) mz 3) rt. You can have other columns in the target lists such as KEGG ID, PubChem ID, Pathway, Chemical Class, SMILES, InChiKeys and so on.
5) Change the sharing setting for the "LCMS" folder to "anyone with the link can access". Copy the link.
6) Submit the link to below Google Form folder. You will receive an email with the processed results.
Once calculations are completed, you will receive an email with the location of results. The calculation time depends on 1) Number of targets 2) Length of Chromatogram 3) and Number of data files. There is no limit on the number of files can be processed by this approach. We can submitted a study with over 5000 data files, and it was completed within 4 hours.