Biological Mass Spectrometry: Proteomics

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Page ID: 79421

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Analytical Sciences Digital Library

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This module is an introduction to biological mass spectrometry with an emphasis on proteomics, the study of proteins, particularly their structures and functions. The first section provides key background information on proteins and proteomics. The second section describes the use of electrospray ionization to determine the molecular weight of a protein using an ion trap mass analyzer. The third section shows how to identify an unknown protein using peptide mass fingerprinting with matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF). The fourth section describes shotgun proteomics and tandem MS experiments for de novo peptide sequencing. An instructor’s manual provides answers to the questions and guidelines for how to implement the activities.

Instructor’s Manual
Section 1: Proteins and Proteomics
- Section 1A. What is a protein?
- Section 1B. What is proteomics?
Section 2: Electrospray
Electrospray ionization (ESI) is a solution-phase “soft” ionization source which converts ions in solution to gaseous ions. The technique is commonly applied to biomolecules and was developed to permit the investigation of analytes from condensed phase samples, such as liquids and solids
- Section 2A. Electrospray and Quadrupole Ion Trap Instrumentation
- Section 2B. ESI-MS Data
Section 3: Peptide Mass Mapping
Often the first step in analyzing a complex mixture of proteins is to separate them using two-dimensional (2D) gel electrophoresis. If 2D gel analysis indicates that new protein is being expressed or the expression level of a protein has changed, that protein must be identified. Peptide mass mapping is a method used to determine the identity of a protein spot in a gel. The protein is cut from the gel, destained, and extracted.
Section 4: MS-MS and De Novo Sequencing
- Section 4A. Tandem MS
- Section 4B. CID of Peptides and De Novo Sequencing

Contributors and Attributions

Dr. Jill Robinson (Indiana University), Dr. Michelle L. Kovarik (Trinity College)