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Anal Chem. 2010 Jan 15;82(2):579-84. doi: 10.1021/ac9018582.

Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry.

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Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, University of California, San Francisco, California 94158, USA.


It is well established that protein sequence determination may be achieved by mass spectrometric analysis of protonated tryptic peptides subjected to collisional activation. When separated by nanoflow HPLC, a high percentage of peptides from complex mixtures of proteins can usually be identified. Recently, alternative, radical-driven fragmentation approaches of electron capture dissociation and the more common electron transfer dissociation (ETD) have been introduced and made widely available. In order to utilize these techniques in large scale proteomics studies, it is important to characterize the performance of these fragmentation processes on peptides formed by a range of enzymatic cleavages. In this study, we present a statistical analysis of the ion types that are observed from peptides produced by different enzymes and highlight the different characteristics of ETD spectra of doubly charged precursors in comparison to precursors of higher charge states.

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