Comparison of Collision Induced Dissociation and High Energy Collision Dissociation for Proteomic Analysis

To comprehensively compare the difference of collision induced dissociation (CID) and high energy collision dissociation (HCD), the tryptic digests of bovine serum albumin (BSA) and cell lysates were analyzed by LTQ-Velos Orbitrap. The HCD fragmentation identified more peptides and this mode showed higher MS/MS success rate and higher Mascot score in the tryptic digests of BSA. The results demonstrated that the HCD fragmentation has higher MS/MS spectra quality than CID. But in the tryptic digests of cell lysates, the CID fragmentation identified more MS/MS spectra, peptides and proteins, which indicated that it produces higher sensitivity. The HCD fragmentation shows higher MS/MS success rate and higher Mascot score distribution, demonstrating higher quality of MS/MS spectrum. Therefore, based on these findings, both CID and HCD modes could be used for large-scale proteomic analysis. The CID mode has higher sensitivity, and HCD mode can achieve higher quality of MS/MS spectrum.