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Volume 16, Issue 1, Pages 15-28

Peptide and protein analysis with mass spectrometry

Sunia A. Trauger, William Webb, and Gary Siuzdak

The Scripps Research Institute Center for Mass Spectrometry and Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA

Copyright © 2002 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Mass spectrometry (MS) is rapidly becoming a fundamental tool for biologists and biochemists in their efforts to characterize cellular function. Recent advancements in MS technology and front-end methodologies, along with the completion of the human genome have greatly popularized its use by researchers for protein identification and characterization. This paper is a general overview of how mass spectrometry is being used for the analysis of peptides and proteins, focusing on its application to molecular weight determination. Sample preparatory and cleanup techniques used in our laboratory for protein and peptide analysis are provided, along with a discussion of data interpretation. The utility of mass spectrometry for protein and peptide analyses lies in its ability to provide highly accurate molecular weight information on intact molecules. The ability to generate such accurate information can be extremely useful for protein identification and characterization. For example, a protein can often be unambiguously identified by the accurate mass analysis of its constituent peptides produced by either chemical or enzymatic treatment of the sample. Furthermore, protein identification can also be facilitated by analysis of the protein's proteolytic peptide fragments in the gas phase; fragment ions generated inside the mass spectrometer via collision-induced dissociation (CID) to yield information about the primary structure and modifications. This overview describes how electrospray ionization (ESI) and matrix‒assisted laser desorption/ionization (MALDI) mass spectrometry is being used for peptide and protein characterization focusing on its application to molecular weight determination.