The contributions of specific amino acid side chains to signal intensities of peptides in matrix-assisted laser desorption/ionization mass spectrometry

Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) analysis of complex peptide mixtures is often hampered by signal suppression effects as well as certain intrinsic properties of specific peptides that influence the desorption/ionization behavior. The present systematic study r...

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Bibliographic Details
Published in:Rapid communications in mass spectrometry 2004-01, Vol.18 (8), p.863-868
Main Authors: Baumgart, Sabine, Lindner, Yvonne, Kühne, Ronald, Oberemm, Axel, Wenschuh, Holger, Krause, Eberhard
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Amino Acids - analysis
Animals
Liver - chemistry
Molecular Sequence Data
Peptides - chemistry
Rats
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods
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Summary:Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) analysis of complex peptide mixtures is often hampered by signal suppression effects as well as certain intrinsic properties of specific peptides that influence the desorption/ionization behavior. The present systematic study reports on the relationship between the occurrence of certain amino acids in peptides and the intensities of the related ions which appear during MALDI‐MS analysis for both tryptic digests of proteins and synthetic peptide mixtures. The analysis of the tryptic digests revealed that the peptide sequences of the most intense peaks detected by MALDI‐MS contained significantly higher proportions of arginine, phenylalanine, proline, and leucine than the average values for the measured proteins. The relationship between the relative signal intensities and amino acid compositions of peptides was studied in more detail by the partial least squares (PLS) method using equimolar mixtures of 144 well‐characterized synthetic peptides. The regression coefficients clearly indicated that the presence of arginine, phenylalanine, leucine and proline tend to enhance the desorption/ionization process which results in higher MALDI‐MS peak intensities. Furthermore, it was shown that the impact of arginine depends strongly on the identity of adjacent amino acids. Copyright © 2004 John Wiley & Sons, Ltd.
ISSN:0951-4198
1097-0231
DOI:10.1002/rcm.1416