Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry

Abstract

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.

Figure 1

Histogram of the frequency of matching ions in ETD spectra as a function of the mass error between theoretical and observed m/z. Data was binned into 0.05 Da intervals. The blue line shows results for all assignments, whereas the red and green lines separate results by charge state of assignment.