Not amenable for positive mode data?

[Former user]

Hi Zhixu Ni,

I've been trying to use the LPPTiger software on some data I acquired using LC-MS/MS in positive polarity. I noticed in the output of the list of oxidized PCs resulting from the in silico fragmentation step are annotated based on the m/z of the [M-H]- species. My questions are i) Can LPPTiger differentiate between positive or negative polarity data inputed to the software? ii) Does it only work for negative polarity data?

[Zhixu Ni]

Hi!

Many thanks for using LPPtiger.

Since there is usually no significant signals for FA residues (especially the oxFA) in positive mode, we do not have a well summarized rule to assign oxPL in positive mode manually.

Thus, the identification of oxPL in positive mode was not developed in LPPtiger. However we do support the identification of oxTG in positive mode in the current development of LPPtiger.

Currently, for the identification of oxPL, we recommend you to use the function from Proteowizard MSconvert to convert only negative mode spectra from polar switching files.

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I hope this might help you to analyze your data.

Best,

Zhixu Ni

[Michelle Saoi]

Hi Zhixu,

Thank you for your prompt response. That’s exciting that the current development of LPPTiger will implement oxTG in positive mode. Do you have an estimate when the next version of LPPTiger will be available? We’d like to be able to test the next version as a lab if that is something you’d like to collaborate on.

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[Zhixu Ni]

Hi Michelle,

We are happy for collaborations!

Please write us with a brief description if it is possible (sample treatment, instruments, what lipids you are looking for…).

My email: [e-mail]

Best,

Zhixu Ni