AMDIS & NIST 2011 December 11, 2012, 01:55:44 PM I will really appreciate if you could answer some of my queries regarding AMDIS. They are as follows,1) Does AMDIS uses retention time to report name of the compounds or it just uses the MS fragmentation pattern to compare against NIST library. I am asking this question because I need to normalise my data with internal standard for any drift in the chromatographic retention time (Only if it uses RT for reporting)2) I am using the internal standard in all my biological & technical replicated. How I can use AMDIS to do data analysis which will account for the RT of my internal standard before processing my data. I have a rough idea about it, that I need to create cal file with internal standard. But it didn't worked for some reason. (I might be wrong). Could you please advise me on this.3) How we do the data normalisation with AMDIS?4) Lastly, I have metabolomic flux analysis experiment where I am using isotopes to monitor the fluxes. Now before I should proceed for my data analysis I need to account for the shift in the masses in order to report true hit. How I can do this with AMDIS? I cannot process any of my data through AMDIS for this experiment as I am not sure how to account for this mass shift?