Dimethyl Isotope-Coded Affinity Selection for the Analysis of Free and Blocked N-Termini of Proteins Using LC−MS/MS

• Published in: Analytical chemistry (Washington) 2007-12, Vol.79 (24), p.9520-9530
• Main Authors: Shen, Po-Tsun, Hsu, Jue-Liang, Chen, Shu-Hui
• Format: Article
• Language: English
• Subjects: Amino acids; Analytical chemistry; Cell Line, Tumor; Cells; Chromatography, Liquid; Deuterium; Formaldehyde; Humans; Isotope Labeling; Methylation; Peptides; Protein Processing, Post-Translational; Proteins; Proteins - analysis; Studies; Tandem Mass Spectrometry - methods
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/ac701678h

Because of enhanced a1 ion signals, dimethyl labeling is useful for identifying the N-termini of proteins or peptides. Herein, we describe a novel strategy that uses dimethyl isotope-coded affinity selection (DICAS) to isolate peptides that contain either the dimethylated or in vivo blocked N-termini of proteins for comprehensive sequence analyses by LC−MS/MS. In this method, dimethyl labeling at the protein level was first performed using formaldehyde-d 2 to label all unblocked protein N-termini and lysine residues, followed by trypsin digestion. The free N-terminal amines of internal peptides generated by digestion were captured by solid supports with aldehyde functionalities through reductive amination. The flow-through fractions, which contained either in vivo or in vitro blocked N-terminal peptides, were subjected to sequence analyses by LC−MS/MS. Owing to the unique feature of a1 signal enhancement associated with dimethylated peptides and the use of the deuterium reagent, the in vitro blocked (or in vivo free) N-termini of proteins could be easily differentiated from the in vivo blocked N-termini. Thus, their sequences and N-terminal modifications could be assigned unambiguously from MS/MS spectra. In this study, the completeness of the labeling and the efficiency of the isolation method were first confirmed by the use of a mixture of model proteins composed of hemoglobin, myoglobin, and α-lactalbumin. The N-termini of all three proteins, including both α and β chains of hemoglobin as well as a signal sequence located in the N-termini of α-lactalbumin, were successfully identified. The protocol was then applied to the analysis of an unfractionated lysate of MCF-7 cells. Results indicate that more than 80% of the isolated peptides contained the N-termini of unique proteins, and many of them were consistent with known or inferred N-terminal processing such as methionine removal and acetylation. In addition, using the DICAS approach, we identified a novel N-terminal formylation for the Ig κ chain V−III region SIE protein and a novel N-terminal signal sequence (1th−32th amino acid) for profilin.