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XCMS Online / mz med
I am using XCMS online for processing and analysing a metabolomic data from UPLC - TOF (Agilent). I have downloaded the XCMS online package from bioconductor, also using R 2.15.2.
Somebody please tell me the best parameters for UPLC TOF [I have used general : retention time format - minutes, feature detection: ppm =10, min peak - 5, max peak - 20,retention time corretion: method - obiwarp,prof Step -1, alignment and statistics kept as default value,Annotation : search for - isotopes+adducts, ppm - 10, Identification: H+,NH4+,Na+]. Then I changed the retension time to seconds, when I checked the result for the cloud plot, It didnt show the feature points the plot.What will be the reason? I changed it into seconds as the limits are 5-20 seconds.
After analysing with this parameters for positive polarity, I met with some issues with diff report
Issue 1 - mz med value in diff report is the normal mass of the compound or with adducts?
Issue 2 - The column METLIN in result.tsv shows many compound names for the same feature. Which one is appropriate to select or do you have any standard scoring system to pick one with max score.
Issue 3 - What is the difference between obiwarp and peak groups.
My objective is to compare the XCMS online result with Mass profile Pro result.
The fast responses will be highly appreciated.
Thank you,
Sithara