LC-MS也用于研究蛋白質組學。在蛋白質組學中,人們遇到的也是要在複合混合物體系中檢測出某些組分并用某種方法確定其詳細結構。用于蛋白質組的自下而上(bottom-up proteomics)的LC-MS方法一般涉及蛋白酶解消化和變性(通常,選用胰蛋白酶進行酶解消化,用尿素將三級結構變性,用碘乙酰胺給半胱氨酸“戴帽”,最后,用LC-MS肽質譜指紋區(peptide mass fingerprinting)或LC-MS/MS串聯質譜去推導各個多肽的序列。[8] )LC-MS/MS通常用于復雜試樣的蛋白質組分析。對于復雜試樣即使用高分辨率的質譜儀多肽的質量也可能發生重疊。像人的血清那樣的復雜生物體液試樣只要首先使用SDS-PAGE凝膠電泳或HPLC-SCX進行分離,都可以在現代的LC-MS/MS系統中操作并且可以定出1000種以上蛋白分子的結構。然而,只有在通過SDS-PAGE凝膠或HPLC-SCX分離樣品之後,這種高水平的蛋白質鑑定才是可能的。
^Combined liquid chromatography mass spectrometry. Part I. Coupling by means of a moving belt interface, Patrick Arpino, Mass Spectrometry Reviews, Vol 8, 1989 pp 35-55
^Increasing Speed and Throughput When Using HPLC-MS/MS Systems for Drug Metabolism and Pharmacokinetic Screening, Y. Hsieh and W.A. Korfmacher, Current Drug Metabolism Volume 7, Number 5, 2006, Pp. 479-489
^Covey TR, Lee ED, Henion JD. 1986. High-speed liquid chromatography/tandem mass spectrometry for the determination of drugs in biological samples. Anal Chem 58:2453-2460.
^Thermospray liquid chromatography/mass spectrometry determination of drugs and their metabolites in biological fluids. Covey TR et al. Anal Chem. 1985 Feb;57(2):474-81
Ferrer, Imma; Thurman, E. M. Liquid chromatography-Time of Flight Mass Spectrometry: Principles, Tools and Applications for Accurate Mass Analysis. New York, NJ: Wiley. 2009. ISBN 978-0-470-13797-0.
Ardrey, R. E.; Ardrey, Robert. Liquid chromatography-mass spectrometry: an introduction. London: J. Wiley. 2003. ISBN 0-471-49801-7.
McMaster, Marvin C. LC/MS: a practical user's guide. New York: John Wiley. 2005. ISBN 0-471-65531-7.