Abstract
Orbitrap mass spectrometry is becoming the popular instrument for proteomic analysis, and HCD mode is becoming the main analysis mode for its high resolution and high sensitivity. This study characterizes the features of HCD spectrum by comparing with CID mode on LTQ Velos Orbitrap. The patterns of b and y ions in HCD and CID modes were systematically compared for the first time, including the charge state, ion frequency and intensity and cleavage selectivity. These results will help develop database search engines and design proper transitions for targeted proteomic analysis in the future.
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