How do I review and edit the alignment of my runs?

The alignment quality measures in Progenesis allow you to review the alignment of your runs so that you can make changes, if necessary. Good alignment is essential for accurate peak detection, so spending a small amount of time reviewing at this screen is worthwhile.

1. Firstly, in the list of runs, click the Score column’s heading to sort them by their overall alignment score, then start by selecting the run with the lowest score.
2. In the Ion intensity map window, zoom in on any areas that need review e.g. those areas highlighted in red in the Ion intensity map window — the Vector editing and Transition windows will now show this area in greater detail.
3. If you can make improvements to the alignment in this area, add a manual alignment vector. Once a vector has been placed, the alignment score should update to reflect this change.
4. Once all areas of the run which need review have been attended to, it’s important to check over the rest of the run too to be sure that the alignment rating of good is correct.
5. Repeat steps 2-4 for the rest of the runs in your dataset.

It’s important to note that vectors affect the alignment quality across the full m/z range for a run so if a run is green all the way across apart from a small red section, fixing the alignment for this section could actually break it for the rest of the m/z range at that RT (particularly if that section contains little or no signal).

If on review of your alignment you actually disagree with the poor alignment rating you can ignore it. It’s important to note that the rating is Needs review as opposed to Poor. Usually the ratings are pretty accurate, but discrepancies can occasionally occur for runs with a large amount of randomly distributed but intense noise. The scores and heatmaps are intended to give you a measure of confidence in the alignment quality, but they don’t actually affect the quantitation.

If review of the alignment shows larger alignment errors or a complete failure to align, you might find the following article more useful:

How do I manually align runs that fail to align automatically?