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Topic: DOUBT ABOUT MS^E (Read 399 times) previous topic - next topic

  • fjnovais
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DOUBT ABOUT MS^E
Hey Folks, I hope things are going well for you.

I have a .raw waters data in a MS^E Mode.

I'd like to know if exists a free-source converter or a R package to convert correctly these raw data into a mzXML or netCDF data, without the necessity of MassLynx software.

Thank you in advance.  :))

Francisco J. Novais
University of São Paulo, Brazil.
  • University of Sao Paulo

  • Jan Stanstrup
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  • Administrator
Re: DOUBT ABOUT MS^E
Reply #1
Msconvert from Proteowizard should be able to do that. Make sure to use the lockmassRefiner filter to get calibrated data.
  • Steno Diabetes Center Copenhagen, Denmark
Blog: stanstrup.github.io

  • fjnovais
  • [*]
Re: DOUBT ABOUT MS^E
Reply #2
Thank you, I'll do that. So the Protowizard can convert properly MS^e data?
  • University of Sao Paulo

  • Jan Stanstrup
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  • Administrator
Re: DOUBT ABOUT MS^E
Reply #3
I have not tried so I cannot answer definitively but I'd think so. Question is if the software you want to use afterwards understands it. I guess you have two "functions"? You could split those apart with the scanEvent filter. You'd need that filter also to get rid of the lockmass scans.

btw.: I had some MS/MS data today where I used the lockmassRefiner. That seemed to do something wrong. On the other hand it seemed that with my data I got the calibrated data which was not the case with previous versions. So for calibrated data compare with your vendor software to check that the peaks have the right mass.
  • Steno Diabetes Center Copenhagen, Denmark
Blog: stanstrup.github.io

  • fjnovais
  • [*]
Re: DOUBT ABOUT MS^E
Reply #4
Yes, my raw data have two "functions":1) "intact compound" m/z ; 2) fragment pattern. Then I'll process them using XCMS R-package.
I'll check the Proteowizard's filters and learn more about these filters that you are telling me. I've been using MSconvertGUI to convert my raw data.
Thank you so much. I was worry about that.
  • University of Sao Paulo

  • cbroeckl
  • [*][*]
Re: DOUBT ABOUT MS^E
Reply #5
Francisco,

The problem with using proteowizard is that I am pretty sure waters tags their MSe data as 'MS1' - the logic being their is no precursor selection.  Since the data are not tagged as MS2, the proteowizard filters do not work.  I use proteowizard whenever i have either MS1 data only, or MS1 data with dedicate MS/MS data.  For MSe I still use databridge run from the acquisition sequence table.  If you have found a solution within proteowizard for MSe with the goal of bringing it to XCMS, do let me know, as I would be very interested in trying it out as well.  

Corey

  • Jan Stanstrup
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  • Administrator
Re: DOUBT ABOUT MS^E
Reply #6
@cbroeckl doesn't it work if you use the scanEvent filter and not the msLevel filter?
  • Steno Diabetes Center Copenhagen, Denmark
Blog: stanstrup.github.io

  • cbroeckl
  • [*][*]
Re: DOUBT ABOUT MS^E
Reply #7
Jan,

I can't say that I remember how this worked, though I think I did try it.  If I recall, the problem is that you have to know which scan events (by integer number) are MS and which are MSE and which are LockMass.  I think that if you have that data, or can extract it in an efficient manner, it would work, but I never figured out an efficient way.  Not to say it can't be done, I just haven't done it.

Corey