Quantitative proteomics has matured into an established tool and longitudinal proteomic experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a new method, Robust longitudinal Differential Expression (RolDE). The methods were evaluated using nearly 2000 semi-simulated spike-in proteomic datasets and a large experimental dataset. The RolDE method performed overall best; it was most tolerant to missing values, displayed good reproducibility and was the top method in ranking the results in a biologically meaningful way. Furthermore, contrary to many approaches, the open source RolDE does not require prior knowledge concerning the types of differences searched, but can easily be applied even by non-experienced users.