IDSL.UFA 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. Generate chromatographic information using the IDSL.IPA package illustrated here for this study

2. Install the IDSL.UFA package using this command: install.packages("IDSL.UFA")

3. Download these pre-calculated IPDBs and use this IPDB for this study IPDB_LipidMaps_pos_005.Rdata. Please note MTBLS1684 is a lipidomics study in positive mode.

4. IDSL.UFA requires 30 parameters distributed into 4 separate sections. For the MTBLS1684 study, use default parameter values presented in the UFA parameter spreadsheet. Next, you should provide information for

   4.1. PARAM0004 for the Address of the IPDB (.Rdata)

   4.2. PARAM0005 and PARAM0006 should be YES

   4.3. PARAM0009 for HRMS data location address (MS1 level HRMS data)

   4.4. PARAM0011 for Address of the peaklists directory generated by the IDSL.IPA workflow

   4.5. PARAM0012 for Address of the peak_alignment directory generated by the IDSL.IPA workflow

   4.6. PARAM0014 for Output location address (MS1 processed data)

   4.7. You may also increase the number of processing threads using PARAM0008 according to your computational power

5. Run this command in R or Rstudio console or terminal: IDSL.UFA::UFA_workflow("Address of the UFA parameter spreadsheet")

6. Your results will be generated at the address you provided for PARAM0014. We suggest using aligned_molecular_formula data from aligned_molecular_formula_table directory to sort the lipid annotations across the entire study.