Protein assignments without peak lists using higher-order spectra

Despite advances in automating the generation and manipulation of peak lists for assigning biomolecules, there are well-known advantages to working directly with spectra: the eye is still superior to computer algorithms when it comes to picking out peak relationships from contour plots in the presence of confounding factors such as noise, overlap, and spectral artifacts. Here, we present constructs called higher-order spectra for identifying, through direct visual examination, many of the same relationships typically identified by searching peak lists, making them another addition to the set of tools (alongside peak picking and automated assignment) that can be used to solve the assignment problem. The technique is useful for searching for correlated peaks in any spectrum type. Application of this technique to novel, complete sequential assignment of two proteins (AhpFn and IC7484-143) is demonstrated. The program “burrow-owl” for the generation and display of higher-order spectra is available at http://sourceforge.net/projects/burrow-owl or from the authors.