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MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Hello Hiroshi

I am working with LC-IMS-MS/MS lipidomics data collected on an Agilent (drift tube) instrument using ramped collision energy. The collision energy was a function of the drift time.
The tutorial works with data that was collected using 3 discrete collision energies. Is there a way I can use MS-DIAL4 for my data?

Thanks
Sneha


Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #2
thanks for the tip. The tutorial uses data dependent MS/MS dataset. Do I have to do anything different from the tutorial since my data is not DDA? It would need some sort of deconvolution.
Can I simply choose 'Data independent MS/MS' in the 'MS method type' field here: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-10-2

I think I would need to do something similar to what is shown here https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#chapter-8
But my question is, instead of 3 fixed collision energies (as described in the tutorial link above), I have a ramped collision energy....so collision energy is different for different molecules based on their drift time.

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #3
Hi Sneha,

if you cannot process your data appropriately, please send me a raw data file that you want to analyze.
In the ion mobility project, the ibf format also contains the information of scan-MSE scan dictionary, and therefore, you do not have to select any additional experimental file as required in normal DIA methods of LC-MS.

Attached is the expected initial setting in start up window of MS-DIAL.
Thanks,

Hiroshi

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #4
Hi Hiroshi

Whats the best way to send you my raw data file? It would be great if you can take a look. The files are large, the Agilent .d file is ~2.8 Gb.

I was able to convert the Agilent .d file to ibf directly using the ibf converter but when I tried to process the file using the MSDIAL, the application closes abruptly. So then I tried converting the .d file to an mzml file using msconvert. But I continue to have the same issue. After entering all the settings , i click finish and see the 'Loading libraries' window briefly and the application closes/crashes.


Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #5
Hi Sneha,

sorry for this late reply.
You can use for example WeTransfer for sending up to 2 GB file.
How about doing this?
1. convert your .d file to ibf with a bit higher intensity threshold to make the file size of ibf small.
2. then, send it to me via the file transfer service.
However, for lipidomics, there may be another issue discussed in the following slot.
http://www.metabolomics-forum.com/index.php?topic=1455.0
Anyway, since I will release new version of msdial on next Monday, your issue can be also resolved by this I hope...

Hiroshi




Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #6
Hi Hiroshi,

Appreciate you being so responsive! I just sent you an ibf file which I created using the ibf converter directly from an Agilent .d file. Let me know if this is a problem and you want me to do  .d-->mzml-->ibf conversion instead.

Best
Sneha


Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #8
Sorry about that, not sure what might have happened. Just resent the file. Also forwarded you the email link you should receive to retrieve the file. Let me know if you dont get it.

Thanks
Sneha

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #9
Hi Sneha,

thanks for sending your ibf data.
What is your problem? Your data could simply be analyzed by MS-DIAL program as attached...
Since your data does not have a calibrant information, you have to add the coefficients to accurately calculate CCS by a single field equation.
Note:
1. please choose profile mode for ms1 and centroid mode for ms2 for your data.
2. if you do not put any coefficient values for CCS calculation, please say "No" after you click the button of "Finish" in the parameter setting window.
3. Currently, I am sorry, even though you set multiple CEs (for example, 0V, 10V, 30V), the current MS-DIAL program for IM-MS data processing only uses 0V (for MS1) and 10V (for MS2) data. The selection of 10V or 30V depends on the function 'order' recorded in the raw data.

Thanks,

Hiroshi

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #10
Hi Hiroshi

Thanks for checking. My issue is that when I select the Lipidomics mode, after I click 'Finish', the program crashes. It works on metabolomics mode but I get no identifications because these are lipid samples. I am using a PC with 16GB RAM so I am not sure what the problem might be. I can try again with the new release of MSDIAL if you think that might help. 

Sneha

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #11
OK, probably, this should be an issue. I have used the latest version (developing one), and it will be uploaded tomorrow.
I will let you know after I upload it on my website.
Thanks,

Hiroshi

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #12
Sounds great, thank you!

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #13
Hi, could you fix your issue by version 4.20?

Hiroshi

Re: MS-DIAL4 for LC-IMS-MS/MS data collected using ramped collision energy

Reply #14
Yes I am able to run the analysis now, thank you!

I am still getting comfortable using MS-DIAL for analysis and might have more questions soon :)