由於電噴灑游離法和基質輔助雷射脫附游離法兩種軟性離子源的發明，使得質譜儀成為蛋白質體研究中相當重要且不可或缺的工具。近年來先進質譜儀及相關技術的發展也使其分析能力漸趨成熟。在本文中將介紹現行各種質譜儀的基本原理及其在蛋白質體分析的應用，其應用範圍包含蛋白質的鑑定和搜尋、蛋白質轉譯後修飾的分析，以及蛋白質的定量等領域。

Since the discovery of electrospray ionization (ESI) and matrix assisted laser desorption and ionization (MALDI),mass spectrometry (MS) has become the major player in proteomics analysis. In recent years, the advances in MS instrumentation and related techniques have greatly enhanced the capability and robustness of MS-based platform for proteomics. In this article, we will introduce the principles of MS and related methodologies for applications in proteomics analysis. The application fields in proteomics will include database assisted protein identification,protein post translational modifications and protein quantifications.