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Topic: MS-DIAL 4.48 for IMS samples (Agilent) (Read 569 times) previous topic - next topic

MS-DIAL 4.48 for IMS samples (Agilent)

Hello.
I am trying to process LC-IM-QTOF data  in the MS-DIAL 4.48, but the time to end has been higher than I was expecting.
I am processing only two lipid samples, because it is only a test. This is my first time with ion mobility, but I have been using MS-DIAL for my first work using lipidomics and orbitrap.

The computer is a desktop with 192 GB of RAM.

Do you have long processing times for ion mobility data ? More than 3-4 hours ?

Thank you.
Ana Carolina Rosa

Re: MS-DIAL 4.48 for IMS samples (Agilent)

Reply #1
Hi Ana,

We've recently worked on a set of Agilent-IMS files for 60 samples with the Ms-dial console app. The total run time was about 12-24 hours starting IBF files, depending on the disk and CPU configuration.

We are using a custom build of the console app with IMS support. Thanks to Hiroshi and Yuki for their help on making it possible!

Wen

Re: MS-DIAL 4.48 for IMS samples (Agilent)

Reply #2
Hi Ana,

which type of instrument do you use right now?
Did you check the noise level of your MS data?
Generally, in addition to IM-MS data, "minimum amplitude cut off" of peak detection tab really affects the data processing time.
Although the default value is currently set to 1000, it is just for our lab's instrumental setting.
So first, try to increase the value to 5000 or 10000, then, check the required time and the result if it makes sense or not.

Thanks,

Hiroshi

Re: MS-DIAL 4.48 for IMS samples (Agilent)

Reply #3
The instrument is Agilent 6560 with IMS and Q-TOF.

But it worked now, thank you!

Re: MS-DIAL 4.48 for IMS samples (Agilent)

Reply #4
Hi Ana Carolina,

Are you running DIA IM-All ions on the 6560 IM-QTOF?
I was testing the new version (4.60) for lipidomics and it looks faster than the previous one for IM data (I did not transform the data to .ibf, just drag & drop the files). However, I could only match CCS values with the lipidomics database. The precursor-fragment deconvolution did not work for such datafiles. I am wondering if there is an additional step for DIA IM-All ions for precursor-fragment deconvolution...

Cheers,
Manuela

Re: MS-DIAL 4.48 for IMS samples (Agilent)

Reply #5
Hi Manuella!
Yes, I am running samples from DIA All ions Agilent 6560 IM-QTOF, though I have not tested this new version yet.
In fact I tried drag and drop the samples but it presented an error.
At the end in the 4.48 version I am able to run 21 samples from positive mode for  around 5 hours and from negative mode 2 hours.
But I will try tomorrow and I can tell you afterwards.

Best,
Ana Carolina

 

Re: MS-DIAL 4.48 for IMS samples (Agilent)

Reply #6
Hi,

I do not validate my program for LC-IM-MS data yet. Maybe, it works. But I will confirm it ASAP.
Thanks,

Hiroshi