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Topic: xcms documentation (Read 1814 times) previous topic - next topic

xcms documentation


first I have to say that I just started using R, I tried to find some answers in this
forum but did not succeed.

I am looking for a documentation of the different methods for feature detection
and their parameters.

Further I do not understand all columns in the peaks table after peak detection:
mz, mzmin, mzmax, rt, rtmin, rtmax and sn are self explaining. But what do
into, intf, maxo, maxf, i and sample mean ?

Regards, Uwe

Re: xcms documentation

Reply #1

R has some extensive documentation in form of manual pages,
they take a bit to get used to, but are well structured.
Check e.g. help("findPeaks.matchedFilter") or help("findPeaks.centWave").

Also, check the papers for more on the algorithm:

  Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and
  Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite
  profiling using nonlinear peak alignment, matching and
  identification, Analytical Chemistry, 78:779-787 (2006)

  Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly
  sensitive feature detection for high resolution LC/MS BMC
  Bioinformatics, 9:504 (2008)

Hope that helped,
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470