%0 Journal Article
%T Optimization of a deep mutational scanning workflow to improve quantification of mutation effects on protein-protein interactions.
%A Bendel AM
%A Skendo K
%A Klein D
%A Shimada K
%A Kauneckaite-Griguole K
%A Diss G
%J BMC Genomics
%V 25
%N 1
%D 2024 Jun 24
%M 38914936
%F 4.547
%R 10.1186/s12864-024-10524-7
%X Deep Mutational Scanning (DMS) assays are powerful tools to study sequence-function relationships by measuring the effects of thousands of sequence variants on protein function. During a DMS experiment, several technical artefacts might distort non-linearly the functional score obtained, potentially biasing the interpretation of the results. We therefore tested several technical parameters in the deepPCA workflow, a DMS assay for protein-protein interactions, in order to identify technical sources of non-linearities. We found that parameters common to many DMS assays such as amount of transformed DNA, timepoint of harvest and library composition can cause non-linearities in the data. Designing experiments in a way to minimize these non-linear effects will improve the quantification and interpretation of mutation effects.