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Topic: Plotted integration-space does match actual integrated area
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Joined: 02 February, 2018
Plotted integration-space does match actual integrated area
May 19, 2018, 04:54:54 PM
I ran into a little a problem and hope someone can help me understanding it.
I used the centWave algorithm of XCMS to detect peaks. That worked generally well. However one of the peaks I found was the one attached. For obvious reasons I looked into it. However, I found the integration indicated by the plot did not match the area given as "into" even close. I extracted the chromatogram to test it and although it looked absolutely the same the area was just different by orders of magnitude. When I tried to find out the reason I saw that rtmin and rtmax confirm the plotted integration boarders. However, scmin, scpos and scmax are all given as -1 which does not really makes sense. lmin and lmax are confirming the values in mzmin and mzmax. Could somebody please explain this to me? I just cant wrap my head around it...
mz mzmin mzmax rt rtmin rtmax into
28945 116.0705011 116.0703547 116.0706169 85.88142934 57.2363598 92.180892 1625626.385
intb maxo sn egauss mu sigma h f dppm scale scpos scmin
1301337.896 7340575 137 0.0340379 335.2332267 2.950305611 7058107.727 56241 0 -1 -1 -1
scmax lmin lmax sample
-1 218 351 5
Ps.: I also wonder how the rt is calculated here. It is neither the average between mzmin and mzmax nor at the highest intensity.
Thanks in advance to all the people who are contributing to this forum.
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