Bifurcating Fragmentation Behavior of Gas-Phase Tryptic Peptide Dications in Collisional Activation

• Published in: Journal of the American Society for Mass Spectrometry 2008-12, Vol.19 (12), p.1755-1763
• Main Authors: Savitski, Mikhail M., Fälth, Maria, Fung, Y.M. Eva, Adams, Christopher M., Zubarev, Roman A.
• Format: Article
• Language: English
• Subjects: Analytical Chemistry; Bioinformatics; Biologi; Biology; Biotechnology; Cations, Divalent; Cell Line; Chemistry; Chemistry and Materials Science; Focus: Peptide Fragmentation; Humans; Medicin och hälsovetenskap; Models, Molecular; Molecular Structure; NATURAL SCIENCES; NATURVETENSKAP; Organic Chemistry; Peptide Fragments - chemistry; Principal Component Analysis; Proline - chemistry; Proteomics; Protons; Stereoisomerism; Tandem Mass Spectrometry; Trypsin
• ISSN: 1044-0305; 1879-1123; 1879-1123
• DOI: 10.1016/j.jasms.2008.08.003

Collision-activated dissociation (CAD) of tryptic peptides is a cornerstone of mass spectrometry-based proteomics research. Principal component analysis of a database containing 15,000 high-resolution CAD mass spectra of gas-phase tryptic peptide dications revealed that they fall into two classes with a good separation between the classes. The main factor determining the class identity is the relative abundance of the peptide bond cleavage after the first two N-terminal residues. A possible scenario explaining this bifurcation involves trans- to cis-isomerization of the N-terminal peptide bond, which facilitates solvation of the N-terminal charge on the second backbone amide and formation of stable b 2 ions in the form of protonated diketopiperazines. Evidence supporting this scenario is derived from statistical analysis of the high-resolution CAD MS/MS database. It includes the observation of the strong deficit of a 3 ions and anomalous amino acid preferences for b 2 ion formation. Statistical analysis supports the hypothesis that the dominant b 2+ ions in CAD of peptide dications are protonated diketopiperazines.