Front Page Forums BioMap Data processing in Axima2Analyze; reading and plotting to Biomap

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    Bogdan Antohe

    This is a cross-posting (both Biomap and Axima2Analyze Forums) as it concerns both the conversion from Axima-CFR output by Axima2Analyze and the way data is read into Biomap.

    Brief description of the process: A raster scan was done with an Axima-CFR and the run file was read into the Axima2Analyze. The output (.img) file was then read into the Biomap software. The Biomap spectra at the various points in the raster scan grid compare well qualitatively to the ones that are obtained plotting directly in the Axima-CFR software. The quantitative comparison does not seem to have any correlation though so I have the following questions:

    1) What information is sent out from Axima-CFR to the run file read by Axima2Analyze? Is it %intensity, mV, area, etc.? Or maybe I should say what information is read by Axima2Analyze from the file generated by Axima?

    2) What is the effect of the parameters set in the conversion window for the Axima2Analyze window? The main parameters are: “Interval” and “Tolerance”. Does it add all the peaks within a range (defined by tolerance) around a point at locations defined by “Interval” and assigns the sum to the mass at that point?

    Also there is a checkbox for “Normalization” which activates two other parameters: “Standard Peak” and “Threshold”. It would be great if somebody could explain me how they work. I have tried several things, but, being at the beginning of my MS work it was not obvious (to me at least) what they do.

    3) When importing the file in Biomap, there is a parameter called “Bin size”. I have noticed that it is used to reduce the number of datapoints (probably to get by the size limitation), but it is not clear what it does to the y axis value in the spectra. Is it adding all the y values for the data points in the “bin”, taking the maximum, or …?

    I am trying to quantitatively match the data seem in the Axima CFR software and the one in Biomap (by the way of Axima2Analyze) and I hope that the answers to the above questions will help me. If there are other things that are needed to understand this, please add them to the list.

    Thank you very much for your help,


    Markus Stoeckli

    BioMap does calculate the average of the intensity values in each bin.


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