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Metabolite Identification Interest Group / Formulating the metabolite identification result via probability
We have developed an unpublished knowledge base tool with the Bandeira lab and it give the ability to do molecular networking but also ID and comparative ID (dereliction as it is called int he natural product community). We simply give an output and then you can rank the hits according to wrong, cannot tell, Compound ID class/possibly correct (isomers etc fall into this) and then correct ID. We let the community tell us what the confidence is as more than one person can subscribe to a data set (this can be thousands of LC-MS runs) and give these star rankings. We also give the overall confidence star rating. In other words build confidence into the software output and it becomes an issue of the past.
Here is a representative link http://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=65349d3bdba24eab93e314ea76765cff&view=group_by_spectrum_all_beta