As a follow up, I have a very hard time separating these peaks and I'm hoping you can shed some light on what I could do differently.
My problem: The peaks getting grouped together have an m/z range of: 153.03701335740, 153.054790674362 --> which is much larger than the 10ppm tolerance that is acceptable in our system to group peaks together. The peaks in that m/z range overlap quite a bit in the 8second window that is defined for that feature, so I can see how xcms could be grouping them together. However, I need the peaks in that feature to be separated into two groups. one group having the mz range: 153.037 - 153.053 and the other group at: 153.0535 - 153.055
I'm using PeakDensityParam and `groupChromPeaks(xset, param=gparam)` to group peaks, and I've tried a range of values for bw, binsize, and maxFeatures with no success. Am I on the right path? Is there anything else you suggest?
Thank you so much for the clarification, CoreyG. You were right - peak grouping was lumping those peaks in with other peaks, which widened the mz window of that feature.
I used the code below on my data, and I detect the following peak group (see screenshot of peaks). However, when I export the feature details, this feature group is not listed (see screenshot of filtered feature definitions). The closest feature group detected is well outside of the retention time window of the peaks plotted. Any help or explanation would be greatly appreciated.
