How to deal with multiple collision energies when using feature based molecular networking

[Jessica Cleary]

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Not sure if this is a question for this forum or for MZmine, but when attempting the Feature Based Molecular Networking workflow on a high resolution data set I am losing library hits that I got when I ran that same data set through the regular molecular networking workflow. I believe this is resulting from the processing with MZmine because we run data dependent analyses on a Bruker qTOF with three different collision energies (12, 48 and 60eV).  So basically I get three different fragmentation patterns for the same precursor ion and they are often very different.  I think maybe MZmine is averaging the fragmentation patterns so that what I end up with is usually the fragmentation pattern of 12eV, which is essentially just high intensity of the precursor ion.

Does this sound reasonable and has anyone encountered this before? Any suggestions as to how I can avoid MZmine averaging the fragmentation patterns or some kind of workaround? Like can I tell it to take only the 48eV (the 2nd MS2scan of a particular precursor ion) as the fragmentation pattern? 

[Louis-Félix Nothias]

Hi Jessica,

The MZmine workflow only outputs in the MGF, the most intense MS2 spectrum associated to each row/feature (in the mz and rt range).

Ideally, we would need to have an MS/MS merger into MZmine itself, and this is something we are going to look into very soon, but this will take sometime.

In the meantime, I would suggest to add the spectrum to the library.

LF

[Vanessa Phelan]

Hi Jessica-

As Louis said, the most intense MS2 spectrum is associated with a feature. If you're using a Bruker qTOF, you can change the data acquisition settings to use the stepping functions instead of set collision energies. Set collision energies work great for ion traps and QQQs, but because you're fragmenting on the fly with a qTOF, the stepping function tends to give better MS/MS spectra for qTOFs. I can give you some settings to start with if you contact me outside the forum.

Best wishes,

Vanessa

[Osama Mohamed]

Hi Vanessa,

I have the same question as I am using 3 fixed collision energies (20,40 and 50 eV) on Agilent qTOF system.

Could you please send me the data acquisition stepping function that you recommends for FBMN better result?

Thanks,

Osama

[Vinícius Galvão Wakui]

Hello colleagues,

I´m actually working with MS data acquired in two fixed collision energies (35 and 70 eV), for the same samples (e.g. for sample 1 at 35 and 70 eV, the same for sample 2, and so on). I´m using FBMN workflow in MZmine 2 to preprocess LC-MS/MS data and I would like to know if it´s correct to use MS data with multiple collision energies to generate molecular networks on GNPS. Or maybe should I analyze the files separately according to their collision energies?

Vinícius 

[Scott Jarmusch]

Hi all,

Has a solution ever been found for picking a collision energy out of DDA with multiple collision energies?

Scott