I need help for metabolites identification from a ion trap GCMS. Can anybody help me out? I have done untarget metabolic profiling. The result look very good. Now I just need to identify the metabolites. It is from seminal plasma.
Look up the mass spec metabolite work of Arun Sreekumar at Baylor Medical School.
The good practice of metabolite identification by MS includes 3 steps. a) Library search (e.g. NIST08, or the like); b) comparison of retention indices (RI) with literature data (e.g. http://www.odour.org.uk/lriindex.html) and c) co-elution of authentic reference substances. If step b) or/and c) is missing the substances have to be named 'tentatively identified'. Regarding this topic see also: MOLYNEUX,R:J: and SCHIEBERLE,P (2007): Compound Identification: A Journal of Agricultural and Food Chemistry Perspective. J Agri Food Chem 55, 4625.
Good luck.
In addition to Ulrich's answer, you may look into MS tables. You need to know the exact molecular weight to the second decimal. The tables indicate which compounds are in that range. This limits to one or two possibilities the identification and facilitates the reference search and controls as indicated by Ulrich.
Dear Kambiz,
try the XCMS database (https://xcmsonline.scripps.edu/) where you can perform your search by fragment, neutral loss or even unknowns (you upload you MS/MS data), or through the Human Metabolome project (www.hmdb.ca) with already >41,000 metabolites in their database. Hope this helps, Ana.
In additonal to above comments, good work usually involves 4 or 5 different separations per sample. Different separations/preparations are better for say aliphatic acid derivatives vs very soluble metabolites. If you are interested in a small group of chemically similar compounds that you might get away with only using a single preparation step.
Dear Ana I have tried out XCMS database. However, I do not get any logical hit. It works for classsification by PCA and etc. However, I do not identify any hit.
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