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zhengfj1994 / MetEx

MetEx is a tool to extract and annotate metabolites from liquid chromatography–mass spectrometry data.
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OSI-SMMS database #2

Open LuShuYangMing opened 1 year ago

LuShuYangMing commented 1 year ago

where can I download the OSI-SMMS database?

zhengfj1994 commented 1 year ago

OSI-SMMS is not open source at present, I'm very sorry for that. My boss entrusted Dalian Dashuo for saling OSI-SMMS, and I only had the permissions for in-house using.

LuShuYangMing commented 1 year ago

Oh, thank you very much! Actually, we have pocessed the data from this article [https://pubmed.ncbi.nlm.nih.gov/31442449/], it provided the raw data and POS or NEG data [https://www.metabolomicsworkbench.org/data/DRCCStudySummary.php?Mode=SetupRawDataDownload&StudyID=ST001231], all data were processed by OSI-SMMS database. The POS or NEG data only have the mz and rt information, but we can not found the correpsonding compounds. Thus, is there a solution to get the compounds based on mz and rt information?

zhengfj1994 commented 1 year ago

I read the article and the data in Metabolomics Workbench. In the article, the authors provided three Supplementary Tables containing differential metabolites. In Metabolomics Workbench, they provided raw peak table which were obtained by XCMS. The raw peak table contains all metabolites (features) whether it's identified or not. In my opinion, you can matched the differential metabolites to the raw peak table by matching m/z and rt. However, they didn't provide identied metabolites without difference, for these metabolites, I don't think there is a good way to get them. It might be possible to email the authors and get all the identified metabolites.