Hi Hong,
I found the source of the problem. The "Peak Finder" module was calculating the
area using retention time represented in minutes, while other modules use
retention time represented in seconds. That is why the areas reported by the
Peak Finder were smaller.
I fixed the module so now it calculates consistently with other MZmine modules.
This fix will be included in the next release of MZmine.
Best regards,
Tomas
On May 11, 2012, at 6:24 PM, Hong Zheng wrote:
Dear Tomas,
Many thanks for your reply, and the attached file is the MZmine project.
Data Analysis Procedure:
LC-MS raw data > mzXML files > Mass detection > Chromatogram builder >
Smoothing > Chromatogram deconvolution > Isotopic peak > Retention time
normalization > Alignment > Gap filling
I don't know whether this is a bug for software or not. Maybe this is just my
wrong analysis method. I hope you don't mind if I make a mistake, and I can get
your help to solve this problem. I really like this software. Thanks a lot for
your time and help! Looking forward to hearing from you.
Have a great day!
Truly yours,
Hong
-----Original Message-----
From: Tomas Pluskal [mailto:plus...@oist.jp]
Sent: 11. maj 2012 03:36
To: Developer discussion
Cc: Hong Zheng
Subject: Re: [Mzmine-devel] Aproblem about the Peak finder in MZmine 2.8
Hi Hong,
Please send us your MZmine project file with the exact steps how to reproduce
the problem (including parameter values).
Then we can take a look at it.
Best regards,
Tomas
On Apr 26, 2012, at 8:02 PM, Hong Zheng wrote:
Dear Developers,
I am a user of MZmine 2 and I very like this software, because it's very
convenient, powerful, and professional. My research interest is the
metabolomics, so this software is useful and helpful to analyze the data. Many
thanks for developing so nice software. Recently, I have downloaded MZmine 2.8
to use. However, when I used the Peak finder in the Gap filling to find the
missed peaks, I found a problem, that is, the area of the new peak is far from
the detected peaks' area, although its height and shape is very similar, as
shown in Figure 1 (in attached file). In Figure 1, the third peak is found by
the Peak finder of MZmine 2.8. I would like to know what's happened? Thanks a
lot for your help, time and patience. Looking forward to hearing from you soon.
Best wishes,
Hong Zheng
<Figure
1.tif>----------------------------------------------------------------
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Tomáš Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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===============================================
Tomáš Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
Fax: +81-98-966-2890
------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
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