Just start to process LC-MS data (.raw) generated by Waters G2S Q-Tof (MSE mode) using a HILIC separation method. A BPI plot was obtained after “Raw data import”, as attached below. I'm wondering:
1. As it showed about 5 signals simultaneously, what are they? MS1 signal? MSE signal? lockspray? noise?
2. How to import just MS1 signal? Can this be achieved by some filters?
As a beginner in this field and the manual of MZmine 2.18.2 was not detailed, could any experienced ones provide imformation on parameter settings? papers, websites, anything is highly appreciated.
1. In the parameter dialog for the BPI plot, you have the option to select which scans to use for the plot, e.g. only MS1 scans. I only see one item in the legend on your plot so you are only seeing one signal. It does however look weird and this is likely something to do with your raw data file or the interpretation of the data in the file. I suggest that you report this issue using the guide provided here: https://mzmine.github.io/support.html#Issues
2. With regards to only importing the MS1 signal, then you have two options:
i. Import the raw file into MZmine and crop the data using the "Crop Filter" under "Raw data methods" -> "Filtering". Most of the modules in MZmine also provides you with the filtering option when you use them so it might not be necessary for you to crop the data in the first place.
ii. Crop the raw data outside MZmine. You can use the msConvert tool from ProteoWizard: http://proteowizard.sourceforge.net/tools/msconvert.html
And I can recommend this tutorial to get you started on preprocessing of LC-MS data in MZmine 2:
https://www.youtube.com/watch?v=VS_Zpyl5chQ
Assuming the data was acquired in MassLynx, the Waters raw data has a number of channels, and it looks like that's what you have there. So if you exported the raw file directly, and you have a UV/ FL detector at the same time, it is possible you have superimposed all of the channels on top of each other. As it is HILIC, I assume you are trying to do something like a released glycan experiment, or else a metabolism or natural product experiment? From the traces it looks like you need some specificity
Thank you both for your replies.
I assume that this problem was attributed to the unique mode of MSE provided by Waters Q-Tof. Therefore, unlike MS/MS mode, different signals could not be separated in MZmine2; then, all of them were showed in the plot when I input 1 for “MS level” and no signal could be found when I input 2, as expected.
For MZConvert tool, I have used ProteoWizard to deal with the same raw data, but don't know whether the fragment information generated by MSE is lost, although the result showed a standard BPI plot in MZmine2.
As St. John Skilton assumed, we do use MassLynx; however, UV or FL detector has not been equipped with UPLC yet.
Now, It seems that we should find some softwares to deal with MSE data. Any suggestion?
- Badges
- Science topic
- Similar topics
- Geoscience
- Cartography
- Mapping