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.

Visualise alignment quality with a simple red/orange/green colour-coded grid overlaid across each run and quality assurance scores

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.

Add a manual alignment vector (red circle and line) and immediately see the effect on alignment quality assurance scores

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?

Choose the individual run (left) or a sub-set of runs such as replicate analysis of pooled samples (right) for more efficient automated data processing