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Messages - joebonic00
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XCMS / Re: m/z value off by 0.1~0.2 Da
Quote from: "Jan Stanstrup"
How did you do the controiding yourself?
They probably use Proteowizard in XCMS online so I guess that is why the mass is off. I have no idea how continuous data is handled there. The way I would get correct files is do one of the following:
1) databridge followed by proteowizard with centroiding enabled
2) my masswolf wrapper followed by proteowizard with centroiding enabled
You can then use xcms online or anything else you want.
Hi Jan, I tried the method you recommended. I kind of get stuck in proteowizard since proteowizard seemed unable to read the .CDF file generated from databridge. I will try the package you wrote to see if it works.
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XCMS / Re: m/z value off by 0.1~0.2 Da
Quote from: "Jan Stanstrup"
How did you convert the files? Proteowizards do not calibrate the data. You can use masswolf or data bridge. See here viewtopic.php?f=26&t=359&p=1694#p1694. I made a wrapper for masswolf that makes it possible to extract each "function" correctly.
Hi Jan,
Thanks so much for your reply. The format of my acquired data is continuum. What I did was just upload the raw file directly to online XCMS since XCMS is compatible with .raw format. However, I found that the m/z values of the processed data were off from my raw data.
The next thing I tried was to convert the continnum file to centroid file before uploading to online XCMS. The processed m/z values were still off. Do I need to convert the .raw file to .CDF by databridge and use the local XCMS?
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