10.1021/ac901108g.s001
Marco L. Hennrich
Marco L.
Hennrich
Paul J. Boersema
Paul J.
Boersema
Henk van den Toorn
Henk
van den Toorn
Nikolai Mischerikow
Nikolai
Mischerikow
Albert J. R. Heck
Albert
J. R. Heck
Shabaz Mohammed
Shabaz
Mohammed
Effect of Chemical Modifications on Peptide Fragmentation Behavior upon Electron Transfer Induced Dissociation
American Chemical Society
2009
activation method electron transfer dissociation
tryptic peptides
peptide sequence coverage
Electron Transfer Induced DissociationIn proteomics
Peptide Fragmentation Behavior
MS
lysine residues
ETD
peptide identification
fragmentation behavior
fragment ion series
ICPL
2009-09-15 00:00:00
Dataset
https://acs.figshare.com/articles/dataset/Effect_of_Chemical_Modifications_on_Peptide_Fragmentation_Behavior_upon_Electron_Transfer_Induced_Dissociation/2827957
In proteomics, proteolytic peptides are often chemically modified to improve MS analysis, peptide identification, and/or to enable protein/peptide quantification. It is known that such chemical modifications can alter peptide fragmentation in collision induced dissociation MS/MS. Here, we investigated the fragmentation behavior of such chemically modified peptides in MS/MS using the relatively new activation method electron transfer dissociation (ETD). We generated proteolytic peptides using the proteases Lys-N and trypsin and compared the fragmentation behavior of the unlabeled peptides with that of their chemically modified cognates. We investigated the effect of several commonly used modification reactions, namely, guanidination, dimethylation, imidazolinylation, and nicotinylation (ICPL). Of these guanidination and imidazolinylation specifically target the ε-amino groups of lysine residues in the peptides, whereas dimethylation and nicotinylation modify both N-termini and ε-amino groups of lysine residues. Dimethylation, guanidination, and particularly imidazolinylation of doubly charged Lys-N peptides resulted in a significant increase in peptide sequence coverage, resulting in more reliable peptide identification using ETD. This may be rationalized by the increased basicity and resulting positive charge at the N-termini of these peptides. Nicotinylation of the peptides, on the other hand, severely suppressed backbone fragmentation, hampering the use of this label in ETD based analysis. Doubly charged C-terminal lysine containing tryptic peptides also resulted in an enhanced observation of a single type of fragment ion series when guanidinated or imidazolinylated. These labels would thus facilitate the use of de novo sequencing strategies based on ETD for both arginine and lysine containing tryptic peptides. Since isotopic analogues of the labeling reagents applied in this work are commercially available, one can combine quantitation with improved ETD based peptide sequencing for both Lys-N and trypsin digested samples.