Abstract
The analysis of acylated proteins by mass spectrometry (MS) has largely been overshadowed in proteomics by the analysis of glycosylated and phosphorylated proteins; however, lipid modifications on proteins are proving to be of increasing importance in biomedical research. In order to identify the marker ions and/or neutral loss fragments that are produced upon collision‐induced dissociation, providing a means to identify the common lipid modifications on proteins, peptides containing an N‐terminally myristoylated glycine, a palmitoylated cysteine and a farnesylated cysteine were chemically synthesized. Matrix‐assisted laser desorption/ionization time‐of‐flight time‐of‐flight (MALDI‐TOF‐TOF), electrospray ionization quadrupole time‐of‐flight (ESI Q‐TOF), and electrospray ionization hybrid triple‐quadrupole/linear ion trap (ESI QqQ~LIT~) mass spectrometers were used for the analysis. The peptide containing the N‐terminally myristoylated glycine, upon CID, produced the characteristic fragments a~1~ (240.4 Th) and b~1~ (268.4 Th) ions as well as a low‐intensity neutral loss of 210 Da (C~14~H~26~O). The peptides containing a farnesylated cysteine residue fragmented to produce a marker ion at a m/z of 205 Th (C~15~H~25~) as well as other intense farnesyl fragment ions, and a neutral loss of 204 Da (C~15~H~24~). The peptides containing a palmitoylated cysteine moiety generated neutral losses of 238 Da (C~16~H~30~O) and 272 Da (C~16~H~32~OS); however, no marker ions were produced. The neutral losses were more prominent in the MALDI‐TOF‐TOF spectra, whereas the marker ions were more abundant in the ESI QqQ~LIT~ and Q‐TOF mass spectra. Copyright © 2006 John Wiley & Sons, Ltd.