Do you have any tips to make automated data processing more efficient?
Alignment Score Column
Order the alignment scores lowest to highest by clicking on the column header in the review alignment table. You can then simply work through the list, editing alignment until you reach a scores threshold that you view as acceptable for your samples.
Alignment scores update with manual editing
Adding manual vectors to a run immediately affects its alignment score in the table so you can quickly decide if it is worth spending time to improve alignment and the try to improve results of comparing relative protein expression between groups.
Set a single run or limited set of runs for the software to choose a reference
Selecting a single run or a limited set of runs that you know routinely produce the best alignment scores reduces the time for automated processing. This minimises the number of comparisons the software performs to find the one with highest similarity to all the other runs in your experiment. See also how do I choose an alignment reference?