Extract metabolite information

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Extract metabolite information

November 02, 2011, 10:00:00 AM

Hi to everybody,
I have somethings in my mind that is unclear about the interpretation of the result obtained using the xcms package for metabolomic data analysis.

Because I have more than two classes I haven't used the diffreport function to extract the most significant peaks according to their ANOVA p-value, but I wrote some code to do this. So I found a small number of signal that are significantly different among the treatment and I use this for the multivariate statistical analysis.

Furthermore the next step was to try to understand if the significative peaks have a "name and surname". To do this I extracted the m/z information from the peak list using the groupnames function and I used the Metabolite Search engine directly from my web browser. I adjusted the ppm error and the polarity.

Now the question: how about the charge state parameter??
In particularly I tried different charge state option: M+H, M+Na, M+K, M+H-H2O... and I studied the results obtained, trying to understand which are the different signal obtained crossing the different data report. For example if the signal 490.1765 m/z has no positive hits with the M+H option, but have a positive hit with the M+Na option, I conclude that is a sodiated adduct instead of a protonated adduct.

Is a correct way to try to identify a metabolite?? Why the diffreport approach has only an M+H information?? Should I use a de-isotoping function to be sure I work only with M+H signal?? Is possible to do this with xcms??

Best

P.S. Sorry for my bad English :oops: I hope you can understand the question/s.

Re: Extract metabolite information

Reply #1 – November 02, 2011, 10:57:58 AM

Hi Ricca,

I recently started playing with metabolomics MS data and I have run into many of the questions you have. First of all, I think that since you are playing with a list of masses, there isn't really a golden standard rule that can lead you to a definite identification of what a peak represents... What you can do is to start restricting the possible interpretations according to your experiments. For example, regarding the charge state parameters, you could restrict your results according to your instrument/experimental configuration so as to obtain an impression of what kind of adducts you expect to have. E.g., for ESI you could possibly restrict yourself to +/-H adducts.

To obtain as much info as possible for your peak list after xcms, you should use the functionalities of CAMERA package which is really helpful(congrats to the authors once again!) and works smoothly with xcms objects. A further grouping according to the theoretical isotope distribution obtained with CAMERA as well as the adduct list should shed some light on your questions. Using the extra info you could obtain monoisotpic masses for several peaks and from there search databases (METLIN, ChEBI, KEGG etc.). I have tried the above so far with a certain rate of success. Good luck!

Panos

Re: Extract metabolite information

Reply #2 – November 02, 2011, 11:02:56 AM

Ricca,

Just quickly before I go home

You might want to check out the CAMERA package from Steffen Neumanns group, also hosted on bioconductor. The package finds correlated peaks and tries to match these to know mass differences, including MH+. Generally speaking, if you see the [M+Na]+ I would expect to see the MH+ ion as well. It'll also give me a lot more confidence that this ion is a [M+Na]+ ion rather than just another MH+ or other adduct of some other compound.

Hope it helps,

Paul

Re: Extract metabolite information

Reply #3 – November 02, 2011, 02:55:19 PM

To get adduct annotations with XCMS Online, just make sure "Search for : isotopes + adducts" is selected in the "Annotation" tab.