Dear folks,
I am going to work on untargeted metabolomics with Agilent QToF. Please suggest to me the best software for untargeted metabolomics.
Thank you!!!!
For quantification, I recommend using an automatic online software like XCMS Online as it's intuitive and easier to use than other chromatogram extraction programs for quantification (https://www.nature.com/articles/nprot.2017.151). If you want to go further, you can check MZmine 2 and check which chromatogram deconvolution algorithm is best for your project (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395). For statistical analysis, check MetaboAnalyst (https://www.metaboanalyst.ca/MetaboAnalyst/ModuleView.xhtml). Now, for Compound ID, you can check both GNPS, one of the largests databases which is actively growing and curated by it's users (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp), or an in silico tool called SIRIUS, state-of-the-art in database-independent chemical formula annotation (https://www.nature.com/articles/s41592-019-0344-8) with other modules used to re-rank molecular formulas with Gibbs sampling, structure and chemical class annotation.
Those are the basics I'm familiar with, but you can explore many tools and check which are useful to answer your biological question.
Dear Dr Naga Veera Yerra,
These softwares may actually help you (MetFrag and XCMS).
Here's their respective links:
https://ipb-halle.github.io/MetFrag/
https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage
Best wishes,
Sabri
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8112213/,kindly check this link.
https://www.researchgate.net/figure/Software-List-for-Metabolomic-Analysis_tbl1_221967731,kindly check this link.
https://www.sciencedirect.com/science/article/pii/S2214030119300203,this link may be helpful.
Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates and products of cell metabolism.
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