Hi all,
I hope i can get a solution to this issue i'm having in XCMS online.
I've been submitting jobs for the last days and for all of the jobs i have received the following note:
"2017-02-14 05:55:48 : Too many features. Processing data without annotation."
Why does this keep happening? I've been analysing urine, serum, liver tissue samples, and frankly, looking at the number of features
they don't look so far off normal. Usually for urine I get around 4000-5000, serum and liver I have around 2000.
In the final table it generates, some of the features are marked as [M+1], [M], sometimes [M+2] and the coresponding in negative mode. This can't be the proper annotation, or full (i might say), because i'm sure there are features there that must be [M+Na], [M+K]... etc.
Any ideas how I could get the annotation to properly work?
Thank you !
I think the XCMS online people rarely come by here so you might consider contacting them directly: https://xcmsonline.scripps.edu/landing_page.php?pgcontent=contact
As for the annotations the isotope annotation and adducts/fragments are two different steps and the adducts/fragments is the computationally intensive one they seem to have limited.
Of course another option would be using XCMS through R so you have control...
Indeed I was refering to the adduct/fragment annotation. I will contact them directly.
I am in the process of setting up the offline R XCMS, I started by using the online version for convenience :).
Thank you very much Jan!