1 research outputs found
MS/MS Spectra Interpretation as a Statistical–Mechanics Problem
We describe a new method for peptide
sequencing based on the mapping
of the interpretation of tandem mass spectra onto the analysis of
the equilibrium distribution of a suitably defined physical model,
whose variables describe the positions of the fragmentation sites
along a discrete mass index. The model is governed by a potential
energy function that, at present, we derive ad hoc from the distribution
of peaks in a data set of experimental spectra. The statistical–physics
perspective prompts for a consistent and unified approach to de novo
and database-search methods, which is a distinctive feature of this
approach over alternative ones: the characterization of the ground
state of the model allows the de novo identification of the precursor
peptide; the study of the thermodynamic variables as a function of
the (fictitious) temperature gives insight on the quality of the prediction,
while the probability profiles at nonzero temperature reveal, on one
hand, which fragments are more reliably predicted. On the other hand,
they can be used as a spectrum-adapted, a posteriori score for database
search. Results obtained with two different test data sets reveal
a performance similar to that of other de novo and database-search
methods, which is reasonable, given the lack of an aggressive optimization
of the energy function at this stage. An important feature of the
method is that it is quite general and can be applied with different
choices of the energy function: we discuss its possible improvements
and generalizations