IDSL.IPA for MTBLS1684 study

Follow these steps for an example study (n=499) MTBLS1684 which has Agilent QTOF 6550 data collected in the RP-ESI-POS mode.

1. Download and install the latest version of R Software from https://cran.r-project.org

2. Optional: Download and install the latest version of RStudio software from https://www.rstudio.com/products/rstudio/download

3. Install the IDSL.IPA package using this command: install.packages("IDSL.IPA")

4. Create a directory, "MTBLS1684" in your hard-drive

5. Download .d raw mass spectrometry files for this case study from https://www.ebi.ac.uk/metabolights/MTBLS1684 and copy the data to the MTBLS1684 directory

6. Use the MS-Convert tool from ProteoWizard to convert the .d format files into the .mzML format

7. IDSL.IPA requires 51 parameters distributed into 9 separate sections. For the MTBLS1684 study, use default parameter values presented in the IPA parameter spreadsheet. Next, Provide address for

   7.1. PARAM0007 for the Input data location address (MS1 level HRMS data)

   7.2. PARAM0010 for Output location address (MS1 processed data)

   7.3. PARAM0041 for Reference file location address which was downloaded from this link

   7.4. You may also increase the number of processing threads using PARAM0006 according to your computational power

8. Run this command in R or Rstudio console or terminal: IDSL.IPA::IPA_workflow("Address of the IPA parameter spreadsheet")

9. Your results will be generated at the address you provided for PARAM0010.