1. An analysis of different types of complementary ion pairs was performed. 2. Based on the specificity of the various ion pairs an intensity ranking was applied prior to database searching. 3. The number CAD/ETD complementary ion pairs increased by using ETD MS/MS data obtained from peptides with different charge states. 4. The approach of intensification was tested on a large dataset containing more than 12,000 unique peptide identifications. 5. Intensified golden pairs of CAD/ETD gives more identification on the protein level then conventional golden pairs. 6. Intensification of complementary ions of CAD-only fragments significantly out-performs traditional CAD data.
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