title: Effects of peptide acetylation and dimethylation on electrospray ionization efficiency.
abstract: Peptide acetylation and dimethylation have been widely used to derivatize primary amino groups (peptide N-termini and the ε-amino group of lysines) for chemical isotope labeling of quantitative proteomics or for affinity tag labeling for selection and enrichment of labeled peptides. However, peptide acetylation results in signal suppression during electrospray ionization (ESI) due to charge neutralization. In contrast, dimethylated peptides show increased ionization efficiency after derivatization, since dimethylation increases hydrophobicity and maintains a positive charge on the peptide under common LC conditions. In this study, we quantitatively compared the ESI efficiencies of acetylated and dimethylated model peptides and tryptic peptides of BSA. Dimethylated peptides showed higher ionization efficiency than acetylated peptides for both model peptides and tryptic BSA peptides. At the proteome level, peptide dimethylation led to better protein identification than peptide acetylation when tryptic peptides of mouse brain lysate were analyzed with LC-ESI-MS/MS. These results demonstrate that dimethylation of tryptic peptides enhanced ESI efficiency and provided up to two-fold improved protein identification sensitivity in comparison with acetylation.
authors.affiliation: Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea.
authors.forename: Kyung-Cho
authors.initials: KC
authors.lastname: Cho
authors.affiliation: Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea.
authors.forename: Jeong Won
authors.initials: JW
authors.lastname: Kang
authors.affiliation: Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Choi
authors.affiliation: Graduate School of East-West Medical Science, Kyung Hee University, Yongin-si, 446-701, Korea.
authors.forename: Tae Woo
authors.identifier: http://orcid.org/0000-0003-0095-3787
authors.initials: TW
authors.lastname: Kim
authors.affiliation: Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea.
authors.forename: Kwang Pyo
authors.initials: KP
authors.lastname: Kim
mesh_terms: D000107:Acetylation; D000595:Amino Acid Sequence; D000818:Animals; D001923:Brain Chemistry; D002853:Chromatography, Liquid / Q000379:methods*; D008745:Methylation; D051379:Mice; D010455:Peptides / Q000032:analysis* / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D010455:Peptides
keywords: LC-MS/MS; acetylation; chemical derivatization; dimethylation; electrospray ionization efficiency