Why is alignment so important?
Alignment makes it possible to accurately compare the compounds in your runs by correcting any drift in retention times. This is done non-linearly across the entire run to give the accuracy needed for fast, statistically robust analysis.
Once alignment has been performed, each run in the experiment will be perfectly aligned so that an ion on run A will be in the same location as the matching ion in run B.
Alignment is arguably the most important part of the CoMet workflow, so any inaccuracies at this stage should be corrected before moving on to peak picking. The alignment views are designed to make finding and fixing any alignment problems as easy as possible.
The screenshots below show a single compound ion in two runs being aligned. Each image shows both runs overlaid on each other; one run is displayed in green and the other is pink. When the runs are not yet aligned (shown on the left), the separate ions are clearly visible. After alignment (shown on the right), the pink and green ions combine to make black when perfectly overlaid.