In this study, we examined a deep learning method for de-identification of clinical notes at UF Health under a cross-institute setting. We developed deep learning models using 2014 i2b2/UTHealth corpus and evaluated the performance using clinical notes collected from UF Health. We compared four pre-trained word embeddings, including two embeddings from the general domain and two embeddings from the clinical domain. We also explored linguistic features (i.e., word shape and part-of-speech) to further improve the performance of de-identification. The experimental results show that the performance of deep learning models trained using i2b2/UTHealth corpus significantly dropped (strict and relax F1 scores dropped from 0.9547 and 0.9646 to 0.8360 and 0.8870) when applied to another corpus from a different institution (UF Health). Linguistic features, including word shapes and part-of-speech, could further improve the performance of de-identification in cross-institute settings (improved to 0.8527 and 0.9052).