AIF data analysis

August 04, 2023, 04:29:39 AM

Hi to all
I have the following doubts about the analysis of All Ion Fragmentation data (AIF) using only 1 energy collision:
I have the following doubts about All Ion Fragmentation (AIF) data analysis:
1) My ms2 data are obtained with only ONE energy collision. I need to use the "SWATH-MS or conventional All-ions method" or I can use the "All-ions with multiple CEs method". If I use the second method, is it correct to use the "Experimental_Information_ForAIF.txt" shown in example 2 (the picture is from the MS-DIAL tutorial)?
2) How can I understand the order and the value in the “experiment” column, since in the tutorial "Tutorial 2. Compound identification in LC-MS AIF data using AMRT MS2 library 191018" is written: "the experiment ID is listed (by order of acquisition, usually vendor-specific)"?

Re: AIF data analysis

Reply #1 – August 07, 2023, 07:35:02 PM

Hi, indeed the order of different scan types is vendor-specific. For example you can check the order in MZmine and if your scan type order is like in the attached screenshot then use your example 2 (ID0: SCAN, ID1: AIF). If you also set "DecTarget" 1 for the SCAN, then you will get deconvoluted in-source fragmentation.