High-throughput identification of mammalian secreted proteins using species-specific scheme and application to human proteome

Secreted proteins are widely spread in living organisms and cells. Since secreted proteins are easy to be detected in body fluids, urine, and saliva in clinical diagnosis, they play important roles in biomarkers for disease diagnosis and vaccine production. In this study, we propose a novel predictor for accurate high-throughput identification of mammalian secreted proteins that is based on sequence-derived features. We combine the features of amino acid composition, sequence motifs, and physicochemical properties to encode collected proteins. Detailed feature analyses prove the effectiveness of the considered features. Based on the differences across various species of secreted proteins, we introduce the species-specific scheme, which is expected to further explore the intrinsic attributes of specific secreted proteins. Experiments on benchmark datasets prove the effectiveness of our proposed method. The test on independent testing dataset also promises a good generalization capability. When compared with the traditional universal model, we experimentally demonstrate that the species-specific scheme is capable of significantly improving the prediction performance. We use our method to make predictions on unreviewed human proteome, and find 272 potential secreted proteins with probabilities that are higher than 99%. A user-friendly web server, named iMSPs (identification of Mammalian Secreted Proteins), which implements our proposed method, is designed and is available for free for academic use at: http://www.inforstation.com/webservers/iMSP/