Dear Grace,
Thank you for the report. Indeed, negative peak areas look very strange.
I found the source of this problem: https://sourceforge.net/p/mzmine/code/3260/
In previous MZmine versions, the peak areas in this module were calculated
using minutes on the RT scale. Since MZmine 2.11 we use seconds on the RT
scale, to make the calculation consistent with other peak detection modules.
Unfortunately, I made a mistake when I was updating the module, that's why you
got negative peak areas. Now I fixed the bug, so MZmine 2.12 will report
correct values.
You can download a fixed version here:
https://www.dropbox.com/s/5l326fu9exwm967/MZmine-2.11.zip?dl=0
Please let me know if you find any further problems.
Tomas
On Aug 24, 2014, at 5:23, Grace Xiaolu Yang
<xly...@stanford.edu<mailto:xly...@stanford.edu>> wrote:
Dear Mzmine developers,
Thank you so much for developing this wonderful tool! I think I found a bug in
the newest 2.11 release. I was trying to do targeted peak picking for my files
acquired on an Agilent QTOF. The .d files were converted to mzXML files by
msconvert, and were imported into Mzmine 2.11. Then I did targeted peak picking
with the following parameters:
Intensity tolerance: 50%
m/z tolerance: 0.0025 m/z or 10 ppm
Retention time tolerance 0.35 absolute min
The peak height values were fine, but the peak area values were all negative
and way too big. I then used Mzmine 2.9 to do the same analysis and the peak
area values were good. I have attached the screen shots of both analysis and
the log message in Mzmine 2.11. I think there is a bug in the targeted peak
picking module in the 2.11 version.
I am using 64-bit Windows 7 operating system. The R version is 2.15.1. All the
R packages are up-to-date. I did not change the HEAP_SIZE setting in the
startMZmine script. Please let me know if you need more information.
Thank you!
Grace
<log.txt><2-9.png><2-11.png>------------------------------------------------------------------------------
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Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
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Fax: +81-98-966-2890
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