How can I correct localised alignment errors?

If, after reviewing the alignment of your runs , you’ve decided you want to make some localised improvements, you’ll need to add some manual vectors:

1. Check that you are set up so your view reflects the alignment being applied by selecting the drop down arrow next to Show Aligned and selecting Always Show Aligned.
2. Zoom in on the Vector editing window so that you can see the ions clearly in the area that needs adjustment.
3. Click and hold on a green ion in the Vector editing window and drag it over the top of the corresponding magenta (reference run) ion – a red box should appear around the ions when they’re overlapped.
   
4. Once you’re happy with the placement, release your left mouse button to place a manual (red) vector. An improvement in alignment should be reflected in an increased score.
   Note: An incorrectly placed vector can be removed by right clicking on it in the Vector editing window.
5. Repeat actions 2-4 for any other areas in any of your runs which need adjustment.
   Note: 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 make it worse for the rest of the m/z range at that RT (particularly if that section contains little / no signal).

See also

• How do I manually align runs that fail to align automatically?
• How do I review and edit the alignment of my runs?
• How can I zoom to an area in the Review Alignment screen?
• How can I prevent my manual vectors snapping to the wrong location?