Hi Anastasia,
The default values have absolutely no meaning. You need to look at your data
carefully and set each parameter according to the characteristics of your data.
The meaning of the parameters is described in the MZmine manual.
If you have further trouble, let me know.
Tomas
On Nov 5, 2010, at 4:00 PM, Anastasia Chasapi wrote:
> Hello,
>
> I was trying the different options of the MZmine 2.1 and I imported one
> .mzXML file with MS1 data. The acquisition was done at a ESI-TOF, using 2
> different energy modes. The problem I faced is that while in the raw data I
> can spot many molecules and in high intensities, when I use the Chromatogram
> builder and look at the peaklist table some of the masses disappear.
>
> For the Chromatogram Builder I used the default options (noise level:default)
> and applied no filtering.
>
> Here is a link to the .mzXML file that I used:
> http://rapidshare.com/files/428879210/140710-104.mzXML.zip
>
> For example there,at time point 3:20, one can see a very intense peak with
> m/z = 453. However, if you go to the peaklist created after the Chromatogram
> builder option, and find the same retention time, the peak is no longer
> there. I already tried to change the options of the Chromatogram builder but
> nothing changed.
>
> Could you maybe help me understand what I'm doing wrong?
>
> Thank you very much
>
> Regards
> Anastasia
>
>
>
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===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology
1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
TEL: +81-98-966-8684
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business during the next growth cycle. Listen Now!
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