As a supplement to immunoassay, mass spectrometry plays an important role in clinical laboratory. With the application and development of mass spectrometry technology in proteomics research, clinical laboratory gradually expanded the analyses of small molecules to proteins/peptides, such as thyroglobulin, insulin-like growth factor-Ⅰ, apolipoprotein E and amyloid protein, etc. However, it faces challenges such as long time and high cost of pretreatment optimization, lack of reference materials and imperfect supervision. Although emerging proteomic biomarkers have been slow to translate into clinical diagnosis, the large proteomic database provides a favorable support for future development.