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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.


Table of Contents

  • Instructor’s Manual (Word, PDF)
  • Section 1: Proteins and Proteomics (Word, PDF)
  • Section 2: Electrospray (Word, PDF)
  • Section 3: Peptide Mass Mapping (Word, PDF)
    • Data File for Section 3: AST4 (Excel)
    • Data File for Peptide Mass Mapping Homework (File)
    • MALDI-TOF Powerpoint Animation (File)
  • Section 4: MS-MS and De Novo Sequencing (Word, PDF)
  • Assessment Questions: For Assessment questions that accompany this module, please contact Michelle Kovarik ( or Jill Robinson (

Developed by:

Dr. Jill Robinson
Indiana University

Dr. Michelle L. Kovarik
Trinity College

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