I am recently working with MZmine 2 software for identification of plant metabolites. I have certain queries on setting the parameters to analyze my results.
I tried using this software, but I think, I hardly know anything about it . I face troubles each time when I need to put parameters such as following:

1. m/z tolerance : How to decide m/z tolerance for steps like Chromatogram builder/ Peak Normalization/ Alignment and so on.
I am using the same value as given in manual( 0.02 -5.0)

2. m/z or RT tolerance Weight:How to decide or what are the bases of deciding m/z weight or RT weight in”Alignment step”? How should I know what is this? “Help” option does not help me either. I used the same as in manual. DO NOT know how correct I am doing.

3. Noise level or Baseline: Is Noise level or baseline same thing? Secondly, How to choose/ decide this? What I understood from “Help”, it is the minimum height of the peak below which every other peak would not be counted. Keeping this in mind, I chose that peak from base peak chromatogram, which shows m/z labeling and is smallest among all the peaks which are labelled with m/z on them. Is this correct way to choose it?

Overall, Please help me understand how to decide the values to fill in parameter box under each step till PCA and log ratio step.

I know this is so much I am asking you, but believe me I a student a biology who never dealt with physics and software like this and on top of that Nobody in my dept. knows how to work with this software not even my supervisor under whom I am working.

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