Instructions

Steps

1. Convert .raw files to .mzML format using the MSConvert software (Proteowizard) adding the filter Peak Picking
   
2. Search if the compound is in the list
   
3. Check the RT and which is the main ion and annotate it in the csv file
   
4. Search if there are MS2 and MSn:
   - if yes & if there is already and html file and new MS/MS to add:
   • delete html
     
   • remove previous MS/MS
     
5. Run:
   - compoundDB
   - molecules
   - stats
   - compoundDB

Folders to check

WATERS/experiments/

• Marynka Raw Files ORBITRAP
  • BARCELONA_MAR
    • standards
      • legumes
        • peptides
          
        • reinnections_dedicated_method
          
        • stds_varis
      • ...
    • ...
  • STD_LIBRARY ...
    
  • ...
• orbitrap_raw_files ...
• ...

... Indicates that the other folders contained in that one still have to be checked.
abcdef Indicates that what it is inside that folder (and subfolders) is already checked.

Last update: 15 May 2022