Hi,
I wish to acquire UHPLC-QTRAP data in scan mode and use XCMS online to process them. I have selected HPLC-single quad as a starting point, but I need to adapt some parameters since UHPLC is to be used (10min gradient). From the pre-defined parameters, I am tempted to change:
1. Feature detection>FWHM, 3-6 sec
2. Feature detection>Step at 0.1or a bit more?
3. Retention time correction>Initial grouping:bw, 3-6?
4. Alignment>bw, 2-4 sec?
All the other parameters would remain unchanged. Does it look acceptable?
And a last question: can XCMS online deal with both centroid and profile data or one is better than the other? I guess if a step window of 0.1 Da is used, centroid would be better?
Thanks for your help,
Best regards
why would you want increase the step size for high res data ?
The other parameters look OK.
If you use centroid mode data, try using centWave for feature detection.
See other posting for more details on that.
Sorry I omitted to mention it: the QTRAP operates at low resolution, like a triple quadrupole. That's why I intend to use the template for HPLC-single quad, but adapt a bit parameters to take into account the fact that UPLC is employed. So I thought maybe an increased step size will perform better.
Could I still use Centwave on low resolution data?
Thanks for you answer
OK, then it makes sense.
Yes, you can still use centWave for low resolution data, you would just have use a pretty high value for the ppm parameter.
Thanks for your reply.