Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics.
Peptide amidination labeling using S-methyl thioacetimidate (SMTA) is investigated in an attempt to increase the number and types of peptides that can be detected in a bottom-up proteomics experiment. This derivatization method affects the basicity of lysine residues and is shown here to significantly impact the idiosyncracies of peptide fragmentation and peptide detectability. The unique and highly reproducible fragmentation properties of SMTA-labeled peptides, such as the strong propensity for forming b1fragment ions, can be further exploited to modify the scoring of peptide-spectrum pairs and improve peptide identification. To this end, we have developed a supervised postprocessing algorithm to exploit these characteristics of peptides labeled by SMTA. Our experiments show that although the overall number of identifications are similar, the SMTA modification enabled the detection of 16-26% peptides not previously observed in comparable CID/HCD tandem mass spectrometry experiments without SMTA labeling.
School of Informatics and Computing, Indiana University , Bloomington, Indiana 47405, United States.
Sujun
S
Li
Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.
Aditi
A
Dabir
Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.
Santosh A
SA
Misal
School of Informatics and Computing, Indiana University , Bloomington, Indiana 47405, United States.
Haixu
H
Tang
School of Informatics and Computing, Indiana University , Bloomington, Indiana 47405, United States.
Predrag
P
Radivojac
Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.
James P
JP
Reilly
D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D007096:Imidoesters / Q000737:chemistry; D008239:Lysine / Q000737:chemistry; D010446:Peptide Fragments / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D013194:Staining and Labeling / Q000379:methods
D000577:Amides; D007096:Imidoesters; D010446:Peptide Fragments; C576674:S-methylthioacetimidate; D008239:Lysine
amidination; chemical modification; fragment ions; logistic regression; mass spectrometry; peptide fragmentation; peptide identification; proteomics