Closed sdrogers closed 4 years ago
@RonanDaly this is the paper the data above is from -- do you think this looks an unusual setup? https://paperpile.com/shared/p8w5Lc
Have done some changes/testings to align format of dia mzXML used in mentioned paper. Copy of code in simple_dia branch https://github.com/kkto28/vimms/commit/7acc2bd0dc40859f27a9e9a20102061bdd6e386f 1) test_controllers.py, using scan_time_dict = {1:0.124,2:0.124} instead of default 2) dia.py added post handling code to replace(hack) scan ms_level to one from two
Captured result is as following.
I am guessing Experimental_Information_ForAIF.txt can be used to differential level 1 or level 2 signals in tools. What I am trying is following configuration, while studying samples by using MSDial. ID MS Type Start m/z End m/z Name CE DecTarget(1:Yes, 0:no) 0 SCAN 65 1500 MS1 21 0 1 ALL 65 1500 MS2 45 1
Reference: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#chapter-8
Been looking at real DIA data, e.g.: https://www.ebi.ac.uk/metabolights/MTBLS1572/files These are created in AIF mode (fragmenting everything). In the mzXML files, all scans are MS1, but every other one has been fragmented. Headers still say MS1. You can see a clear pattern in the output (look at intensities in following plot), and the scans themselves iterate between fragment and non-fragment.
At the moment, we cannot generate such data, but we need to be able to to make AIF like this.
Possible fixes:
- Hack the MS-level of the MS2 scans back to MS1 when they get returned to the controller (feels mucky)
- If a scan is passed to the simulator which has a collision energy >0 always return MS2 peaks and not MS1?
This is, I think, only a problem in the simulator. In the real MS, we can pass MS1 scans with collision energy and it will just fragment.
I think we've partly got to the bottom of this...
And a couple of further points of clarification:
Been looking at real DIA data, e.g.: https://www.ebi.ac.uk/metabolights/MTBLS1572/files These are created in AIF mode (fragmenting everything). In the mzXML files, all scans are MS1, but every other one has been fragmented. Headers still say MS1. You can see a clear pattern in the output (look at intensities in following plot), and the scans themselves iterate between fragment and non-fragment.
At the moment, we cannot generate such data, but we need to be able to to make AIF like this.
Possible fixes:
This is, I think, only a problem in the simulator. In the real MS, we can pass MS1 scans with collision energy and it will just fragment.