Dansylation of tryptic peptides for increased sequence coverage in protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric peptide mass fingerprinting

A database search using peptide mass fingerprints obtained by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry leads to protein identification with incomplete sequence coverage, because certain peptides are preferentially desorbed/ionized and some are not detected at all. We show that certain tryptic peptides mainly with C-terminal arginine not detected before derivatization become detectable upon dansylation. Others, mainly with C-erminal lysine, are suppressed. An increase in protein sequence coverage and protein identification score by combined data from underivatized and dansylated peptides in database search is demonstrated using human amnion proteins (human serum albumin precursor, calmodulin, collagen alpha 2(VI) chain precursor, galectin-3) separated by two-dimensional gel electrophoresis as well as femtomole amounts of BSA in solution. Copyright (C) 2005 John Wiley & Sons, Ltd.