Parameter settings for Fast DDA scan on a Water's Xevo G2-S Q-TOF

[dko...@gmail.com]

Hello.  I've finally got my first GNPS run to actually work.  That said, I see some issues with the parameters I'm using to pick peaks to MS/MS.

Often times, the selected MS/MS will not be the true parent peak.

Attached is a photo with the mass selected in the top right of the window, showing that 256.24 was sent for fragmentation, while the actual parent peak is 258.19

I have screen shots of every window with my inputs into the DDA Parameters, but was wondering if there was a compiled list of suggested peak-picking for MS/MS conditions for each instrument vendor, or in my particular case of interest, the Xevo G2-S.

I've attached all parameters I last ran with, excluding the "exclude and include" list as they don't apply right now as I want to target anything and everything present in a decent level in the sample.

While I have yet to get MSe to convert into a pseudo MS2 for use in GNPS, the DDA seems to work well.

Thanks, Dakota

I hope to start contributing spectra soon, have over 6,000 fractions of Actinomycetes fermentations.

[Louis-Félix Nothias]

Hi Dakota,

Were you able to find a solution to your problem with the Xevo data ?

[Dakota Hamill]

Not yet.  Still unsure of the best way to select masses.  Isotope patterns, intensity, adducts etc.    

Also wondering how much going up to the 30 scans degrades data quality or if the Xevo can handle it.  

Effectively I'm worried the DDA scan won't always pick the same masses each run.  

Just looking for suggested parameters for the Waters DDA for bacterial fermentation extracts.  Wouldnt be a bad idea to have a wiki of standard parameters for all machines somewhere so consistent data starts to build off the same machines with same fragmentation energy etc. 

On Mar 21, 2018 4:56 PM, "Louis-Félix Nothias" <louisfeli...@gmail.com> wrote:

Hi Dakota,

Were you able to find a solution to your problem with the Xevo data ?

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[Pieter Dorrestein]

Glad to hear it is working you. I think the parent mass difference is something you should ask waters about. We dont have a waters instrument. What we have seen with other instruments is that this was the difference between pre-calibration from which DDA selects ions and calibrated data using a lock mass when it is finally displayed.

It will be spectacular to see a molecular network with 6,000 samples from actino's. If you have issue with running at that scale send me an mail as we have strategies behind the scenes that allow ups to partition the job and might be needed. 

P

[Dakota Hamill]

I'll call Water's and see about optimizing DDA the next time I'm in front of the machine.  I remember meeting you Pieter at the Cambridge meeting last year by the Boston mass Spec society hosted by Bruker.  I want to start contributing to GNPS, but still learning the ropes.  An updated tutorial would be helpful but I may make one myself anyway with what works for a Water's machine.

Right now I'm basically manually entering and searching high rez masses into the Search All submitted databases with +/- 0.1 m/z and it's really really slow.  Dictionary of Natural Products was down for me today otherwise, that's what I do on there as well, again, tediously slow.  But, this is for my MSe runs which can't seem to be optimally converted.  The few DDA runs I did I was finally able to use molecular networking for once and find some matches.

It'd be great to have a way to enter multiple masses and just give a plus or minus mass variance for quickly searching masses of interest without the need to upload spectra.  Also when hovering the cursor over the spectral window to look at exact masses of the spectra, the cursor often times won't appear or will only appear if hovered over the bottom 5% of the m/z line.  

I think GNPS is the foundation for something great, but can use work in making it easier to understand how to search your own data and how to submit your own data.   I'll do what I can to propose and submit a solution rather than just complain!  Making LCMS databases more accessible to the "normal" scientist would be game-changing.  I know many people that use GNPS are highly specialized and highly trained but a majority of people with access to great potential samples to submit may not have that training or the time or patience to stick with it and learn the system.

Thanks, Dakota.

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[qinp...@gmail.com]

Hello, l also run LC-MS/MS on Waters for GNPS analysis and Struggle for the parameter settings for Fast DDA scan on a Water's Xevo G2 Q-TOF, have you found the appropriate parameter for Fast DDA? 

Besides,i found some different in GNPS between DDA and MSE acquired, do you compare DDA and MSE in the same sample?

Thanks,

Lu

在 2018年2月4日星期日 UTC+8上午3:52:00，dko...@gmail.com写道：