I can use peak.getScanNumbers().length to get the amount of data points over
the chromatographic peak when I use the targeted peak detection. However, if I
use the chromatogram builder or GridMass peak detection to generate a peak list
then all peaks are listed to have 2531 data point (= the amount of MS scans in
the raw data file). Only when I do a chromatogram deconvolution, the number is
listed as the correct value.
Should we leave this as it is or is it a mistake in the chromatogram builder
and GridMass peak detection modules?
/Thomas
-----Original Message-----
From: TFRD (Thomas Franck Dyrlund) [mailto:t...@steno.dk]
Sent: 16. april 2015 11:57
To: Developer discussion
Subject: Re: [Mzmine-devel] Quality control of MS peaks
I guess that will then be the next MZmine challenge for me :-)
I have added the RT start, RT end and # data point from the current data model.
Any comments?
https://github.com/mzmine/mzmine2/compare/master...dyrlund:qcdata
/Thomas
-----Original Message-----
From: Tomas Pluskal [mailto:plus...@oist.jp]
Sent: 16. april 2015 06:15
To: Developer discussion
Subject: Re: [Mzmine-devel] Quality control of MS peaks
Hi Thomas,
# data points and RT start/end can be obtained from the current data model.
The other values can be added, but if you do so, you will need to modify
multiple implementations of the Feature interface, and also you will need to
update the project loading/saving modules accordingly. It will take a bit of
coding, but it is certainly possible.
Best,
Tomas
Adding these values to the current data model is possible, but you will have
> On Apr 15, 2015, at 20:28, TFRD (Thomas Franck Dyrlund)
> <t...@steno.dk<mailto:t...@steno.dk>> wrote:
>
> Hi all
>
> I’m interested in adding these peak information to the peak list tables in
> MZmine to be used for QC of peaks:
> - # data points
> - RT start/end
> - FWHM
> - Tailing factor
> - Asymmetry factor
>
> I think the best way would be to add a module under the peak list methods
> which can calculate the values for a peak list. I’m however not sure if this
> is possible with the current data model and would like to know what you think
> and if you have any comments or suggestions. If it is not possible with the
> current data model then I would like to add this as an option under the
> export methods.
>
> Best,
>
> Thomas
>
> ____________________________
>
> Thomas F. Dyrlund
> Post Doctoral Researcher
> Research, Systems Medicine
>
> Steno Diabetes Center A/S
> Niels Steensens Vej 2-4
> DK-2820 Gentofte
> Denmark
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>
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Tomas Pluskal
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1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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