Hi,
I'm looking for some resources to find good parameter settings for the
centwave algorithm. I'm using orbitrap data.
I tried the search function of this forum, but found no hints.
Regards, Uwe
Uwe,
Try looking at the old google groups page.
https://groups.google.com/forum/#!searc ... UhJfaiK6IJ (https://groups.google.com/forum/#!searchin/xcms/orbitrap$20parameters/xcms/sEsirr0OJOY/obUhJfaiK6IJ)
The main parameters on centWave are peak width and the ppm parameter. I believe I'm correct in say that most of the orbitrap people use the default ppm value. However, the peak width parameter will vary greatly on the LC method you're using.
Hope it helps, let me know how you get on.
Paul
I tried the default parameter ppm=25 but then I get warnigs about insertion
problems. What does this mean ?
Regards, Uwe
Hi Uwe,
these "insertion problems" occur if you have two masses very close (defined implicitly through the ppm parameter) within
a single mass spectrum. Usually with centroided data, that should not happen (by definition...).
In Orbitrap data that might happen due to the Orbitrap typical symmetrical artifacts (shoulders)
around high abundant peaks, and possibly the centroiding algorithm used by Thermo. If there is only a few hundred, that is not a serious problem,
and you could reduce ppm to, say, 10-15 ppm. Tens of thousands would hint at a profile spectrum.
Yours,
Steffen
Hello,
i am writing my master thesis in ecology and try to analyse FTICR-MS data.
Since I never analysed statistically LC/MS data before and I am qite new to R I would be very thankful if anyone can provide me with the R code to determine the optimal parameters.
Is Centwave even the right method? What about MassSpecWavelet?
Many thanks and kind regards,
Uwe
P.S.: I used LTQ-FT (Thermo Fisher) and converted the Xcalibur raw files with Xcalibur to net.CDF
Addendum:
I used MSConvert to create centroid data from the Thermo raw data. Let's see what happens with "ppm=5" ...
Unfortunately no peaks have been found.
Please help!
Now I'm trying: xset<-xcmsSet(steps=1,profmethod="bin") ...
XCMS online worked!