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Topic: XCMS peak picking (Read 6646 times) previous topic - next topic

XCMS peak picking

Hello,

I am unsure of how XCMS extracts ions and I would really like to understand it. For example, when the instrument takes snap-shots while running samples, one ion can come at several different masses which are a little different (under the same peak) i.e. 107.1043, 107.1057, 107.1068, etc. When XCMS extracts these ions, does it consider them separate or one and the same ion?

Thank you very much!

Majda

Re: XCMS peak picking

Reply #1 –
XCMS will group these peaks into a feature if they appear to "belong together".
It is normal to observe slightly different m/z values in consecutive scans.
centWave will them pick them up if the difference is less than the "ppm" input parameter.
Please see the centWave paper for more details.

Re: XCMS peak picking

Reply #2 –
Thank you, Ralf, for your comment.

I was asking that question because I have a concern regarding the data extraction. I extracted some data, job ID 4274 and there is a pretty prominent peak with a mass of 177.103, which we know is cotinine. When I look at the raw chromatograms, it is there. However, after extracting the data, it does not make the list. Maybe my parameters are not set up correctly. Is there anything you can do to help me resolve this issue?

Thank you very much!

Majda

Re: XCMS peak picking

Reply #3 –
What type of instrument are you using ?
Have you tried increasing ppm ?

Re: XCMS peak picking

Reply #4 –
Hi Ralf,

sorry I never saw that you posted this reply back in May. I am still having the same issue with a mass not being extracted in XCMS but it does come through using Mass Lynx.

The instrument we are using is UPLC-ESI-QTOFMS. Can you tell me please what XCMS parameters you think I should try to tweak in order for cotinine to come through?

THank you very much!

Majda

Re: XCMS peak picking

Reply #5 –
The UPLC/QTOF parameterset should work fine. Is that the one you used ?

If yes, is it possible that the missing peak is oversaturated ?

Re: XCMS peak picking

Reply #6 –
Yup, that is what I used and I don't believe it is oversaturated. I am having this issue with some of our masses of interest not being extracted but they are when I use Mass Lynx. I don't understand XCMS well enough yet to be able to "intelligently" tweak parameters, but I have tried playing with them..but still nothing in terms of getting the masses I am interested in.