July 25, 2012, midnight by Sonya Alexandrova
Topics: Computational Mass Spectrometry
In “Inferring Protein from Spectrum”, we inferred a protein string from a list of b-ions. In practice, biologists have no way of distinguishing between b-ions and y-ions in the simplified spectrum of a peptide. However, we will often possess a pair of masses in the spectrum corresponding to a single cut. The two corresponding ions complement each other: for example, mass("PR") + mass("TEIN") = mass("PRTEIN"). As a result, we can easily infer the mass of a b-ion from its complementary y-ion and vice versa, as long as we already know the parent mass, i.e., the mass of the entire peptide.
The theoretical simplified spectrum for a protein
$P$of length $n$is constructed as follows: form all possible cuts, then compute the mass of the b-ion and the y-ion at each cut. Duplicate masses are allowed. You might guess how we could modify “Inferring Protein from Spectrum” to infer a peptide from its theoretical simplified spectrum; here we consider a slightly modified form of this problem in which we attempt to identify the interior region of a peptide given only b-ions and y-ions that are cut within this region. As a result, we will have constant masses at the beginning and end of the peptide that will be present in the mass of every b-ion and y-ion, respectively.
Say that we have a string
Given: A list
Return: A protein string
1988.21104821 610.391039105 738.485999105 766.492149105 863.544909105 867.528589105 992.587499105 995.623549105 1120.6824591 1124.6661391 1221.7188991 1249.7250491 1377.8200091