Problem with annotation of lipidomics data MSDIAL v. 4.9.221218.

January 18, 2023, 11:59:56 AM

Hello all,
I came across a problem when annotating lipidomics data from Thermo instrument (.raw) using the latest MSDIAL version 4.9.221218. On average, I see ~70% fewer reference matched annotation compared to version 4.90 when using the same parameters (same parameter file) on the same raw data. Both versions detect roughly the same total number of features but the number of ref. matched is ~70% less in v. 4.9.221218

Here is an example using commercially purchased brain extract:
v. 4.90:
Total number of features: 8606
ref. matched: 852
v. 4.9.221218
Total number of features: 9688
ref. matched: 202

Interestingly, I only observed this using Thermo data. Processing Sciex data worked OK.
Is there something that needs to be changed as far as processing parameters go for the latest version vs version 4.90?

Thank you,
Vladimir.

Re: Problem with annotation of lipidomics data MSDIAL v. 4.9.221218.

Reply #1 – January 19, 2023, 05:56:34 AM

I have the same problem with Thermo Mass Spectrometer.

Re: Problem with annotation of lipidomics data MSDIAL v. 4.9.221218.

Reply #2 – February 10, 2023, 03:52:08 AM

Hi, maybe it is worth to writing all parameter from scratch rather than importing a file from an older version.
Best, CP

Re: Problem with annotation of lipidomics data MSDIAL v. 4.9.221218.

Reply #3 – February 13, 2023, 03:55:34 AM

Goodmorning, yes, I meant writing all the parameters from scratch.
The error persists.

Thanks.

Andrea Garbarino