Comparing Spectra with the Spectral Convolution solved by 1043

July 31, 2012, midnight by Sonya Alexandrova

Topics: Computational Mass Spectrometry

Comparing Spectra

Suppose you have two mass spectra, and you want to check if they both were obtained from the same protein; you will need some notion of spectra similarity. The simplest possible metric would be to count the number of peaks in the mass spectrum that the spectra share, called the shared peaks count; its analogue for simplified spectra is the number of masses that the two spectra have in common.

The shared peaks count can be useful in the simplest cases, but it does not help us if, for example, one spectrum corresponds to a peptide contained inside of another peptide from which the second spectrum was obtained. In this case, the two spectra are very similar, but the shared peaks count will be very small. However, if we shift one spectrum to the right or left, then shared peaks will align. In the case of simplified spectra, this means that there is some shift value $x$ such that adding $x$ to the weight of every element in one spectrum should create a large number of matches in the other spectrum.


A multiset is a generalization of the notion of set to include a collection of objects in which each object may occur more than once (the order in which objects are given is still unimportant). For a multiset $S$, the multiplicity of an element $x$ is the number of times that $x$ occurs in the set; this multiplicity is denoted $S(x)$. Note that every set is included in the definition of multiset.

The Minkowski sum of multisets $S_1$ and $S_2$ containing real numbers is the new multiset $S_1 \oplus S_2$ formed by taking all possible sums $s_1 + s_2$ of an element $s_1$ from $S_1$ and an element $s_2$ from $S_2$. The Minkowski sum could be defined more concisely as $S_1 \oplus S_2 = {s_1 + s_2 : s_1 \in S_1, s_2 \in S_2}$, The Minkowski difference $S_1 \ominus S_2$ is defined analogously by taking all possible differences $s_1 - s_2$.

If $S_1$ and $S_2$ represent simplified spectra taken from two peptides, then $S_1 \ominus S_2$ is called the spectral convolution of $S_1$ and $S_2$. In this notation, the shared peaks count is represented by $(S_2 \ominus S_1)(0)$, and the value of $x$ for which $(S_2 \ominus S_1)(x)$ has the maximal value is the shift value maximizing the number of shared masses of $S_1$ and $S_2$.

Given: Two multisets of positive real numbers $S_1$ and $S_2$. The size of each multiset is at most 200.

Return: The largest multiplicity of $S_1 \ominus S_2$, as well as the absolute value of the number $x$ maximizing $(S_1 \ominus S_2)(x)$ (you may return any such value if multiple solutions exist).

Sample Dataset

186.07931 287.12699 548.20532 580.18077 681.22845 706.27446 782.27613 968.35544 968.35544
101.04768 158.06914 202.09536 318.09979 419.14747 463.17369

Sample Output



Observe that $S_1 \oplus S_2$ is equivalent to $S_2 \oplus S_1$, but it is not usually the case that $S_1 \ominus S_2$ is the same as $S_2 \ominus S_1$; in this case, one multiset can be obtained from the other by negating every element.

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