Potential bug reading Thermo RAW files (DDA) for versions 4.9

February 02, 2024, 08:14:07 AM

Hello,

I was working wit MS-DIAL v4.9 (because I like to save my spectra in txt files and export .MAT files which I can't do with versions 5+) and I had a problem with lot of spectra. The spectra are coming from LC-Orbitrap (so Thermo .RAW files) acquired in DDA with inclusion list. I imported the files without conversion and for a lot of the peaks the MS2 was missing some fragments. I am enclosing an example where you can see on top how the spectra should be (from Thermo software FreeStyle). In the middle you can see the raw and deconvoluted spectra from MS-DIAL v4.9 (missing the 78.98 fragment). And below you can see the same spectra extracted using MS-DIAL v5.1.
It looks like my problem was solved by using MS-DIAL 5.1+ so that's not a big problem for now but I just wanted to let you know that it looks like MS-DIAL v4.9 do not extract correctly the MS2 information from my files (before going to versions 5+ I tried tweaking Peak picking and MS2Dec parameters and it made no changes). The problem looks worst in negative ionization than in positive ionization for me.

Cheers
Jean