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IE-Omics

iterative exclusion script for generating exclusion lists from previous runs

IEomics and III Manual: For users

Step 1: Locate Necessary Programs Innovative Omics Software

• R, use the version with this distribution: IE_Omics_AND_III\R-3.3.3\bin\x64\Rgui.exe
• MSConvert (ProteoWizard), use the version with this distribution: IE_Omics_AND_III\msconvert64\MSConvertGUI.exe

IEomics:

Step 2: File Conversion in MSConvert

• MS2 for R script
  • Upload .raw
  • Peak Picking (Vendor): Level: 2-2 (not Vendor for waters)
  • msLevel: 2-2
  • threshold: absolute .0001 most intense
  • Output: MS2

Step 3: Run the script

• Open the code ([date]_IEomics.R) and after looking at the notes on the top of the script enter: Ctrl+Shift+S (or Ctrl+A and run), you can copy from a text editor and paste into R console.
• A number of pop-up boxes will appear, read the dialogue box and enter the correct information. After the final pop-up box is entered a file will appear in the directory in which you imported the .ms2 files from. Note that pop-up boxes may appear behind all open windows, so minimize all open windows if pop-up boxes are not obvious.

Step 4: Import exclusion list into the Thermo Methods File (for Thermo, other vendors methods vary)

• Import the generated exclusion list into the thermo methods file
• Change the exclusion tolerance to 100 ppm (recommended) or the exclusion tolerance desired
• Save the method file under a new name, and make sure to modify the sequence by adding the new method file
• Reinject the sample with the new ddMS2-topN Method with the imported exclusion list
• Repeat from Step 2.