This module performs baseline correction on raw data files. It is designed to compensate for gradual shifts in the chromatographic baseline by detecting the baseline and then subtracting it from the raw data intensity values. The module proceeds as follows for each raw data file passed to it:
If the base peak chromatogram was used then the corrected intensity values are calculated as follows:
Icorr = max(0, Iorig
- Ibase)
If the TIC chromatogram was used then the corrected intensity values are calculated as follows:
Icorr = max(0, Iorig
* (1 - Ibase / Imax))
where Iorig, Ibase, Imax and Icorr are the original, baseline, maximum and corrected intensity values, respectively, for a given scan and m/z bin. If Ibase is less or equal to zero then no correction is performed, i.e. Icorr = Iorig.
This module relies on the R statistical computing software being installed and two "packages" being installed in R:
install.packages("ptw")
install.packages("rJava")
You will also need to correctly configure several environment variables in your MZmine start-up script (startMZmine_Windows.bat, startMZmine_Linux.sh or startMZmine_MacOSX.command):
[1] | Boelens, H.F.M., Eilers, P.H.C., Hankemeier, T. (2005) "Sign constraints improve the detection of differences between complex spectral data sets: LC-IR as an example", Analytical Chemistry, 77, 7998 – 8007. |