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XCMS Online / XC-MS data analysis: MS/MS matching –replicates- and methods
Our objective is the identification of the metabolites present in plant extracts and compare their accumulation levels in ctrl vs treatment.
After loading the data in the XC-MS website:
1) Which is the most suitable method to analyze LC-MS ESI triple quadrupole data?
2) Saying that I used HPLC orbitrap method in pairwise job (ctrl vs treatment), is there a way to group the replicates. (In the heatmap etc..)
3) The identification using MS/MS matching, the matrix model is limited to: human, mouse, fly, and yeast. However we are looking for plant secondary metabolites. Is there a way to change the matrix model?
Thanks in advance