Detection of therapeutic peptide is a major research direction in the current biopharmaceutical field. However, traditional biochemical experimental detection methods take a lot of time. As supplementary methods for biochemical experiments, the computational methods can improve the efficiency of therapeutic peptide detection. Currently, most machine learning-based therapeutic peptide identification algorithms do not consider the processing of noisy samples. We propose a therapeutic peptide classifier, called weighted echo state networks based on subspace projection (WESN-SP), which reduces the bias caused by high-dimensional noisy features and noisy samples. WESN-SP is trained by sparse Bayesian learning algorithm (SBL) and introduces a weight coefficient for each sample by kernel dependence maximization-based subspace projection. The experimental results show that WESN-SP has better performance than other existing methods. © 2023 The Author(s). Published by Elsevier B.V.