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Messages - chemyumen

3
MS-DIAL / Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)

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Quote from: Hiroshi Tsugawa on
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
4
MS-DIAL / Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)
Quote from: AnaCarolina-RosadaSilva on
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 
7
MS-DIAL / 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
9
MS-DIAL / how to select NAGlySer as available lipid class in MS Dial 4
Dear MS Dial developer,

In the recently published paper, 'MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas', 117 lipid subclasses were made available for lipid identification. NAGlySer is one of them and it's a good news for me since it's quite abundant in the bacteria I study. The problem is I can't seem to find it in 'identification' tab. Any suggestion on how to find and select it?

Regards

Shuai