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Topic: MS-DIAL 4.48 for IMS samples (Agilent) (Read 307 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!