Skip to main content ↑ ↓

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - Marco

1
XCMS / Re: Processing direct infusion data using MassSpecWavelet
Thank you for reply Ralf. This is what I try.

But for example, when I try to change the scales, then R writes

" scales 1 is to large"

 I tried other scale numbers, for example less than 1 and more than  1, and it repeats this message with the value I entered.

As I said, I am not an expert in R and bio informatics, but willing to learn.

best wishes,
Marco
2
XCMS / Re: Processing direct infusion data using MassSpecWavelet
Hi everybody, maybe I have to precise my post.

So, I take direct infusion single scans and I want to compare these Scans (only 1 against 1, or a average of 10 Scans) of different samples. I measure in a mass range of 150-2000, but also in smaller ranges on an OrbitrapXL.

xs <- xcmsSet(
  method="MSW",
  files=mzdatafiles,
  scales=c(1,4,5),
  nearbyPeak=FALSE,
  verbose.columns = FALSE,
  winSize.noise=50,
  SNR.method="data.mean",
  snthr=0.001
)
xsg <- group(xs, method="mzClust")
xsg


What I get as result are only a few masses, with a bad resolution. It would be great, when someone could help me.

best wishes,
marco
3
Other / Re: Convert qgd files from shimadzu into mzXML
Hi, thank you for your help!!!
@ Steffen,
 Saving as .cdf was possible using the vendor software.

@Jan
openchrom would also work, but firstly I wanted to try without contacting our IT-department to install new software.

Best wishes,
Marco
5
XCMS / Processing direct infusion data using MassSpecWavelet
Hi,
I have a question concerning the dataprocessing with the package "MassSpecWavelet". I use direct infusion at a OrbitrapXL and I am interested in low molecular masses (<2000 Da). To compare different sets I need a good tool and hence I know xcms from LC/MS analysis I tried xcms using the package "MassSpecWavelet". But it seems that it does not work. I have to say that I am not an expert in R. Problem what I got was that not all peaks I see in the xcalibur file are listed. Probably it is because of the noise which is calculated in the package. But I would like to list all mass peaks also the low ones to do not overlook minor compounds. Is it  possible in general with these package?  If there is anyone who can help me would be great.

Best wishes
Marco