Towards Mass Spectrum Analysis with ASP

TL;DR

This paper introduces a novel approach using Answer Set Programming to determine molecular structures from mass spectrometry data, employing canonical representations to efficiently explore possible structures.

Contribution

The work develops a new ASP-based method with canonical structure representations to improve mass spectrum analysis, outperforming existing symmetry-breaking techniques and commercial tools.

Findings

Correctness validated on known molecular structures

Outperforms existing ASP symmetry-breaking methods

Competitive with commercial analytical chemistry tools

Abstract

We present a new use of Answer Set Programming (ASP) to discover the molecular structure of chemical samples based on the relative abundance of elements and structural fragments, as measured in mass spectrometry. To constrain the exponential search space for this combinatorial problem, we develop canonical representations of molecular structures and an ASP implementation that uses these definitions. We evaluate the correctness of our implementation over a large set of known molecular structures, and we compare its quality and performance to other ASP symmetry-breaking methods and to a commercial tool from analytical chemistry. Under consideration in Theory and Practice of Logic Programming (TPLP).