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Topic: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper) (Read 814 times) previous topic - next topic

Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Hi MS Dial team,

I'm reanalyzing some Bruker TIMS-TOF PASEF data from the MS Dial 4 nature biotech paper in 2020 to get familiar with processing ion mobility data. There are many cases where two identical lipids at same retention time were reported. One has CCS value while the other has "-1" as CCS. See picture below. Just wondering which one I should trust or they are all real? And how I can filter if one of them needs to be removed.

Regards

Shuai

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #1
Any people have similar issue when analyzing ion mobility data for lipidomic project?

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #2
How did you convert and import the data?
T.

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #3
Hello, I am working with ion mobility data (from agilent LC-IM-QTOF) and this happened as well.

I only excluded all the -1 compounds, it seems for me that it is a bug from the system and the lipids are duplicated.

Hope it help you.


Best Regards,

Ana Carolina Rosa

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #4
How did you convert and import the data?
T.
I used the ibf converter which comes with MS Dial 4.60 and selected ion mobility as data type.

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #5
Hello, I am working with ion mobility data (from agilent LC-IM-QTOF) and this happened as well.

I only excluded all the -1 compounds, it seems for me that it is a bug from the system and the lipids are duplicated.

Hope it help you.


Best Regards,

Ana Carolina Rosa
Hi Ana, thanks for the reply. Just checked the MS Dial tutorial again and it seems that the same lipid is reported twice, once in RT vs m/z dimentions and once in ion mobility vs m/z dimentions. So far, it doesn't like there is any easy way to filter out one of these two groups within MS Dial data viewer.

Shuai 

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #6
Dear users,

Sorry for my late action. Yes, Shuai is right.

As the procedure of MS-DIAL, the program detects the peak in the RT axis. Then, the ions are expanded in the drift axis. Then, the peaks are detected in the drift axis. The row containing -1 value means that this is the result of RT axis peak detection. Therefore, you will see the same RT results twice.

Now, for bruker tims-tof data, you do not have to convert .d file into ibf. (I hope)
From next version (it will be uploaded in the mid of July), the MS-DIAL also supports the direct import of .d file containing pasef data.
You can evaluate it by the following link. (the link is expired on 4 July, 2021)
https://we.tl/t-Cv77aUpHIj

Hiroshi

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #7

[/quote]
Dear users,

Sorry for my late action. Yes, Shuai is right.

As the procedure of MS-DIAL, the program detects the peak in the RT axis. Then, the ions are expanded in the drift axis. Then, the peaks are detected in the drift axis. The row containing -1 value means that this is the result of RT axis peak detection. Therefore, you will see the same RT results twice.

Now, for bruker tims-tof data, you do not have to convert .d file into ibf. (I hope)
From next version (it will be uploaded in the mid of July), the MS-DIAL also supports the direct import of .d file containing pasef data.
You can evaluate it by the following link. (the link is expired on 4 July, 2021)
https://we.tl/t-Cv77aUpHIj

Hiroshi
Hi Hiroshi,

Thanks for the reply and link. Will test it for the DDA PASEF lipidomic data from our TIMS-TOF Pro and let you know if there is any issue.

Shuai

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #8
Hi Hiroshi,

Just downloaded the test version of MS Dial 4.68 and tried to import .d file (DDA PASEF data) from Bruker TIMS-TOF Pro. But this version of MS Dial still only allow .ibf file to be imported. I selected ion mobility as separation type.

Regards

Shuai

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #9
Hi Shuai

Please directly drag & drop your .d files into the data grid in analysis file setting window.
You do not have to click the browse/select button.

Because .d file is recognized as a folder in the normal file browser dialog, I cannot provide the environment to recognize the .d file as a file format at this moment soon. Therefore, instead, I allowed the drag/drop option right now.

Hiroshi

 

Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

Reply #10
Hi Hiroshi,

It works now! Thanks. Will update if I have more questions.

Regards

Shuai