Hello,

I'm using find xcms::findChromPeaks with centwave algorithm to extract XICs for which I need to input a roilist, I was testing using just one ROI or m/z Trypto<-data.frame("mz"=216.1341,"rtmin"= 50, "rtmax"= 900,"mz"=216.1341,"scmin"=51,"scmax"=800,"mzmin"=216.1321,"mzmax"=216.1361,"length"=20,"intensity"=1000)

but I keep getting the following error...Error in validObject(.Object) : invalid class “CentWaveParam” object: 'roiList' does not provide all required fields!

I don't know what I am missing! please help

The roiList parameter should be a list. So what you should do is to provide the ROI as:

Trypto <- list(c(scmin = 51, scmax = 800, mzmin = 216.1321, mzmax = 216.1361, length = 20, intensity = 1000))
cwp <- CentWaveParam(roiList = Trypto)

Note however that it would be much easier to extract the ion chromatogram for your compound of interest in the following manner (assuming that data is your data object, i.e. the data you read with readMSData):

trypto <- chromatogram(data, rt = c(50, 900), mz = c(216.1321, 216.1361))

Parameters rt and mz allow to define the retention time and m/z range from which you want to extract the data. The data is then returned as a Chromatograms object. You can simply call plot on that object to plot the data, or you could also run findChromPeaks on that object to perform a chromatographic peak detection on that extracted chromatogram.

hope this helps

cheers, jo