I'm using Waters Acquity UPLC-Synapt G2 Mass spec for the analysis of the whole metabolite from a group of cell lines. The technician provides '.RAW directory' as raw data and '.cdf' file as the result. Both files processed successfully in XCMS online. But the result shows many identification names (Multiple hits) in Meltin search. How to avoid multiple hits in XCMS online? What is the best tool to analyze MSE data?
Hi Joseph,
this is technically a very up to date system. Congratulations. It seams that you are new to MS data evaluation. Maybe you start reading on metabolite annotation as defined by the metabolomics standards initiative.
In short: you measure a set of ion masses (MS spectrum) and their secondary fragmentation products (MSe) at a certain retention time of your LC run. Based on these data and potentially by comparing against data bases/libraries of standards an algorithm tries to decide which compound was causal for the observed data. Here, multiple hits are rather the general rule than the exception in non-targeted assays. So you *don't want to* avoid multiple hits.
Regarding your second question: do you intend to use MSe for annotation purposes or something else? Do you want to work GUI based or on a command line? Which problem do you try to solve?
Bests, Jan
Hi Jan Lisec
Thank you so much for your help.
Yes, I used MSE for annotation of metabolites. I'm not much familiar with R programming and command line tools, I prefer GUI based platforms.
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