Hi Zac,
There's an R package named "targetedmsqc" that does what you're describing. It calculates a number of metrics describing peak quality (symmetry, peak shape similarity, jaggedness, modality, co-elution, etc ...) and outputs an ensemble score based on the totality of the features for each transition. The current version uses Skyline reports as input and generates a csv file with columns for features and quality score. We are working on a version that allows for integration of tMSQC output as an annotation file into Skyline and hoping to release it within the next month. Please see this publication for more details if you're interested: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173846/
The package is available here along with instructions on how to use it: https://github.com/shadieshghi/TargetedMSQC
Best,
Shadi