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The contributions of specific amino acid side chains to signal intensities of peptides in matrix‐assisted laser desorption/ionization mass spectrometry
Author(s) -
Baumgart Sabine,
Lindner Yvonne,
Kühne Ronald,
Oberemm Axel,
Wenschuh Holger,
Krause Eberhard
Publication year - 2004
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.1416
Subject(s) - chemistry , mass spectrometry , desorption , amino acid , peptide , matrix assisted laser desorption/ionization , chromatography , arginine , ionization , leucine , phenylalanine , proline , matrix (chemical analysis) , analytical chemistry (journal) , ion , biochemistry , adsorption , organic chemistry
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.