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Messages - Paz Cortes

1
XCMS / Re: peak picking error
Ralf,
Thank you very much for your help.
I think you are right, it's probably a saturation problem.
2
XCMS / Re: peak picking error
We use a S1200 LC - Q-TOF Agilent 6520 instrument.
We first change the output format from .d to .mzXML using msconvert.
(msconvert data.d --mzXML --filter  "peakPicking true 1-" --filter "threshold absolut 100 most-intense")
Then we process it using XCMS, using centWave for peak detection using default parameters except for ppm.
We figured out that the ppm window we were using was to narrow.
When we use ppm = 15 for the detection our peak is not picked.
Using a larger ppm (ppm=30 or ppm=50) the peak is detected, however we get around 30.000 "data insertion problem" warnings. Are that many warnings acceptable?


Here are  the plots of the ROIs from the peak in question and the eic plot.
Thanks very much for your help

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3
XCMS / peak picking error
hi,

I have tried to use centWave to find peaks in my data. I used a run with a known compound in it. I know at which m/z and rt values I should find it. Plotting EIC with m/z range and time range around those values I can see a clear peak. However it is not detected by centWave. I used default parameters and ppm= 15.
Any ideas?

Paz
5
CAMERA / CAMERA question
Hi,
I've recently been looking into the CAMERA software for isotope and adduct annotation.
I have done tests using the default adduct ruleset but now I would like to know how to add other features to that list.
I notice xsAnnotate objects have a "ruleset" slot . Should I change this data.frame to add other features?
And if so, what is stored in the oidscore, quasi and  ips columns?

Thanks for your help,