I got some questions regarding my metabolomics research from a reviewer, he/she suggested me to provide a table of the authentic standards as supplementary. I asked the cooperators who helped in the metabolomics analysis, they said it is impossible since they use their own dataset to analyze the data and there is plenty of spectrum for each metabolites. They suggested me to give the information of the significant expressed metablites （including VIP FC P-value m/z rts ） Is there any good idea to answer the reviewer's question? Thanks in advance!
Hi,
we also had collaborative metabolomics studies with the other partner. They always sent us an EXCEL sheet displaying the parameters including mz, time, VIP, FC, P value, compound name etc. I think you should communicate with your partner for analysis again (they might think you need all the data from their database) and request for the data of significance in your study. Hope you can sort it out soon!
Best
Dear Li
I may be wrong, but I think this reviewer's comment is not so tough as it looks. Perhaps, they just want to see if any of annotated metabolites you report were confirmed by analytical standards. For this, you can just ask your collaborators to provide the list of compounds (only names... and maybe vendor) they have used to create their own in-house library.
Dear Li Zhou, it is a common problem in LCMS analysis when one wants to assign an identification to observed chromotographic peaks. Unlike in GCMS analysis, ionization of the eluting compounds is not standarized and the resulting mass spectra are not library searcheable. Your options to identify the compounds depend for a large part on the technical parameters of the equipment used and the skills of the operator. For instance, if a well calibrated Orbitrap is used as the MS, chemical composition calculations can shed light on the chemical formula of the eluting compound. Accurate mass can help inmensely, but is not a panacee. The fragmentation pattern, knowledge about the preferred ionization (M+H, M+Na, M-H etc) may help excluding unlikely candidates. The most simple way is to run the verified standards and compare the retention time, accurate mass and fragmentation pattern (which is heavily dependent on the ionization potential of possible coeluting compounds!). I hope this is helpful. Feel free to ask for clarification wherever needed. Kind regards, Harrie Verhoeven
And I forgot to mention the analysis of the stable carbon isotopes. Since Carbon is defined as mass 12, the C13 which is present as 1,3% of the main C12 isotope, will be present in your mass spectrum for each fragment containing carbon. The relative intensity of the m/z +1 peak versus the m/z peak indicates the approximate number of carbons of the fragment. Some elements, like sulfur, have more and more abundant stable isotopes, which will result in a strongly correlating intensity of the m/z, m/z +1, m/z+2 values. This is a very helpful way to look at mass spectra and can help to eliminate many possible identifications at first hand analysis. Good luck!
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