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Centwave optimal parameters

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

Re: Centwave optimal parameters

Reply #1 –
Uwe,

Try looking at the old google groups page.
https://groups.google.com/forum/#!searc ... UhJfaiK6IJ
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
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: Centwave optimal parameters

Reply #2 –
I tried the default parameter ppm=25 but then I get warnigs about insertion
problems. What does this mean ?

Regards, Uwe

Re: Centwave optimal parameters

Reply #3 –
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
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

Re: Centwave optimal parameters

Reply #4 –
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

Re: Centwave optimal parameters

Reply #5 –
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") ...

Re: Centwave optimal parameters

Reply #6 –
XCMS online worked!