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Messages - bo2014

4
XCMS Online / Default parameter setting for UPLC-G2S MS
Hi,
Does anyone know why the default value for prefilter intensity is 500 and for noise is 0 in XCMS Online? Usually, how should we change the default value?
Thank you in advance.
Best regards!
Bo
5
XCMS / Re: Noise parameter for findPeaks.centWave
Hi Jan,
Thank you very much for your reply.
Below is a MS1 spectrum. Whether I can set the value according to this spectrum? For example, set the value of noise = 300?

On the other hand, if we have data from blank sample that generated in the same LC and MS conditions, whether we can set the value of noise according to the intensity level from this data?

Best regards!
Bo

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8
XCMS / Re: XCMS for UPLC-Waters G2-S Q-TOF
Quote from: "Jan Stanstrup"
Some impressions:
  • An overlooked parameter is the step size. It can be set with profparam = list(step=0.005). The default of 1 (!?) is way too high. See http://metabolomics-forum.com/viewtopic.php?f=8&t=576 for a brief explanation.

    Hi Jan,
    Thank you very much for your answers.

    I have checked the parameter "profparam", it's only useful for profile data. If the data I provided is centroid, then I don't need to set the parameter. Is that true?

    Best regards!
    Bo
9
XCMS / XCMS for UPLC-Waters G2-S Q-TOF
Hi All,
Does anyone know how to set the parameters of XCMS for the data generated by UPLC-Waters G2-S Q-TOF?
My code is below, is it good for that data?
xset<-xcmsSet(cdffiles,
                        method="centWave",
                        ppm=15,
                        peakwidth=c(2,25),
                        snthresh=10,
                        prefilter=c(3,500),
                        mzCenterFun="wMean",
                        integrate=2,
                        mzdiff=0.01,
                        noise=0,
                        verbose.columns=TRUE,
                        fitgauss=FALSE,
                        sleep=0,
                        polarity="positive"
                        )
Best regards!
Bo