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Messages - capkavl

2
MS-DIAL / No support for custom .msp library in the Lipidomics workflow in MSDIAL 4.9...
Hello all,
We made a custom .msp lipidomics library and would like to use it in MSDIAL 4.9.221218. However, in the lipidomics workflow, the program does not allow us to select the .msp file. The select button takes you to lipid subclass slection but does not allow us to browse to the library file. We tried to paste the path to the .msp file in the selection box but upon processing, this link is ignored and a default, build-in library is used instead.
Does anyone have any advice on how to solve this problem?
Thank you,
3
MS-DIAL / Problem with annotation of lipidomics data MSDIAL v. 4.9.221218.
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.
4
MS-DIAL / Re: Problems with Lipidomics mode: No peaks/zero ref matches
Actually, I'm seeing something similar when processing Thermo .raw data using the latest 4.9.221218 version. I see severely under-annotated results. When processing the data using v. 4.90 I do not see this problem. Please try to process your data using v. 4.90.
Also, I do not see this problem when processing Sciex data.
I hope this helps.
Vladimir.
5
MS-DIAL / Adding Internal Standards to LipidBlast DB to be used in MSDIAL
Hello,
We would like to use Ultimate SPLASH internal standard mix with MSDIAL. Since this version of SPLASH is not supported by MSDIAL, we would like to add the components to the LipidBlast library to be searched and annotated by the software and then do normalization in post-processing. This could be also used for adding additional internal standards that are not part of supported SPLASH mixes.
Are there any suggestions on how to best add these compounds to the LipidBlast library to be then used in MSDIAL?
Thank you,
Vladimir.
7
MS-DIAL / Re: How to export alignment result in mztab-M format
Thank you Biswa and Hiroshi for your comments. I gave it another try today but I am getting the same error with the latest version of MSDIAL. I select mztab-M option in addition to the raw area data and the error appears and then MSDIAL crashes. The same happens when combining with a normalized data export (while making sure the data is normalized). Please see the screenshot of the error. Are there any other parameters prior to exporting that need to be correct for this to work?
Thank you,
Vladimir.
8
MS-DIAL / How to export alignment result in mztab-M format
With recent versions of MSDIAL, I see there is an option to export data in mztab-M format. We would like to use this format but when I try to export alignment data using this option (while no other options are selected), no file gets generated. If there is another option selected (such as Normalized data matrix) in addition to mztab-M option, an error is displayed and MSDIAL crashes.
Is there any solution to this?
Thank you,
Vladimir.