Data Management And Sharing System of China National Clinical Research Center for Neurological Diseases
Statistical characterization of HCD fragmentation patterns of tryptic peptides on an LTQ Orbitrap Velos mass spectrometer
First author：Shao Chen, Zhang Yang
Corresponding author：Sun Wei
essential_information
- Person in charge：Shao Chen, Zhang Yang
- Data Sources： OTHERS
- Number of papers：OTHERS20190280
- Published time：2014-06-16
2014-06-16
Published articles
Journal：Journal of Proteomics
Publication type: Research Article
IF(IF): 4.044
PMID: 24981973 Link To Pubmed Full text Download
Background And Purpose
Method
In this study, b and y ion fragmentation patterns and residue-specific cleavage effects in HCD mode were statistically characterized on a LTQ Orbitrap Velos mass spectrometer. We compared HCD and CID spectra collected in an Orbitrap for the same doubly and triply charged tryptic peptides.
Conclusion
These results will assist with the development of database search engines and the design of proper transitions for targeted proteomic analysis.
Main results
Our analytical results revealed novel statistical features of HCD spectra. The intensity of y ions reached a maximum in the 60–70% and 40–50% relative mass bins of HCD spectra from doubly and triply charged peptides, respectively. The HCD mode showed a slight preference for generating y ions with lower charges than did CID mode. Singly charged fragment ions dominated the five fragment ions with the highest intensity in HCD spectra. Hydrophobic residues for b ions were the primary differences in cleavage selectivity between the two modes, while residues for y ions showed a similar cleavage preference.