Error-minimization approach to reduce protease bias

Inhalt:
The main goal in proteomics is to describe the proteome in a comprehensive and accurate way, and enzymolysis is a key step in the process of large-scale proteomics experiments. For the same protein samples, using different proteases may introduce a strong bias into protein analysis results. This situation will make proteomics experiments irreproducible and will have a serious impact on the experimental results. To reduce this protease bias, we present EMQ (Error-Minimization-based Quantification for Protein), an approach based on error minimization. In contrast to the existing method, our model includes information on shared peptides, which are ubiquitous in mass spectrometric datasets. The abundance of shared peptides will be assigned to related proteins accurately, thereby determining the protein abundance. Based on this feature, we used the proposed model with several datasets, and compared its performance with the other. Finally, our model is shown to have better performance than other approach (average Pearson correlation of ~0.83 obtained by EMQ, while ~0.63 by other model).