Formalin fixed and paraffin embedding(FFPE) is the most commonly used technique for clinical tissue preservation，while FFPE tissues have the characteristics including standardized preparation process，easy to store，large sample quantity and retrospective clinical information，which make them the high quality library for biomarker discovery and verification.In recent years，a series of proteomics approaches have been developed，covering sample preparation，protein digesting，peptide separation and identification by mass spectrometry.The whole processes have the characteristics of micro scale sample quality，high sensitivity and high throughput.These methods have been successfully used in clinical proteomics researches，for example，the tumor precision medicine.The proteomics methods for FFPE tissue samples and their applications in oncobioloby are summarizd in this review，providing a valuable reference for proteomics based clinical precision medicine researches.