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The Chemical Educator

ISSN: 1430-4171 (electronic version)

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Abstract Volume 9 Issue 5 (2004) pp 272-275

Ladder Sequencing of a Peptide Using MALDI-TOF Mass Spectrometry

Owen A. Moe,* Walter A. Patton, Yun K. Kwon, and Mollie G. Kedney

Department of Chemistry, Lebanon Valley College, Annville, PA 17003,
Received July 20, 2004. Accepted September 2, 2004.

Published online: 16 Sepember 2004

Abstract. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, an important new mass spectral technique for the analysis of biomolecules, has revolutionized experimental approaches in the biochemical sciences. We describe an experiment that demonstrates C-terminal ladder sequencing of a peptide, one of a myriad of new applications of MALDI in the area of protein chemistry. In this experiment students use carboxypeptidase Y to generate C-terminal cleavage products (ladders) of a tetradecapeptide, followed by MALDI analyses to determine the masses of the ladder components. From mass differences between successive peptide products, students determine the first seven amino acids from the C-terminal end of the peptide. They then resolve ambiguities in the sequence and identify the source of the peptide using the online BLAST search/alignment algorithm.

Key Words: Laboratories and Demonstrations; biochemistry; MALDI; C-terminal sequencing; carboxypeptidase; ladder sequencing; BLAST

(*) Corresponding author. (E-mail:

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Issue date: October 1, 2004

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