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Topics - pennoca

1
MS-DIAL / identification score cut off in lipidomics experiment
Dear all,

I noticed that by lowering the score cut off I can identify more internal standards (equisplash) in my samples.

When I look at the spectrum I see that the Rev Spectrum similarity is pretty good and probably the identification problems lies on some contaminated peak at the low mass range.

In the data collection tab, it is possible to define the MS/MS mass range begin and end, however, I have a felling that this parameter is not taken in consideration for the MS/MS scoring calculation and may explain why I can detection ISTD only low (80%) score cut off.

I was wondering if MSDIAL uses the info in MS/MS mass range begin and end to ignore the contaminating ions during score calculation?

Cheers,
Carlos. 
2
MS-DIAL / handling double identification
Dear community,

In a typical lipidomics experiment there are many double identificatiosn, usually lipid with different retention times but same MS1 and MSMS. How are you handling such double ID lipids? Similarly, I noticed that deuterium labelled lipid standard from Splash are also double identified. Have you also experience this? I am usually filtering double identified lipid out of the data but sometimes the internal standard is also filtered out (it happen quite often for LPCd7 and LPEd7 in positive mode).

Well it would be great to exchange on this.

Best regards, Carlos.
3
MS-DIAL / Lipidomics in cell lines, reproducibility
Dear community,

It may be off the topic here but I will give it a try.

I was wondering if anyone could point me to good references from labs performing lipidomics analysis in cell line which are cultivated in media containing FBS. We have an issue with reproducibility, I believe it has to do with the fact that cells are exposed to lipids from FBS in the media. How do you control for this ? Is it recommended to starve the cells for lipidomic studies (for how long)? Or do you fast the cells? Any protocol you know?

It would be great to exchange experiences with you on this.

Best regards, Carlos.
4
MS-DIAL / MSDIAL version 4.18 vs 4.12
Hey all

I  processed exact same files using the two version of MSDIAL (4.18 and 4.12) and identical data processing parameters. There are few lipid classes are not identified in the 4.18, for instances, CL and CE, maybe there are other, I did not look deeply.
Is this expected ? are you experiencing same ?

Thanks and best,