Many practically relevant inorganic solution systems have complex compositions with tens or hundreds of distinct species. Here, we present an approach to analyzing ESI-MS spectra combining a set of scripts for peak assignment and a quantum chemical methodology for the determination of the structure of selected ions. We selected solutions of CuCl, PdCl ₂, and the CuCl-PdCl ₂ mixture as models of popular precatalysts in cross-coupling reactions and the Wacker process that can form “cocktail”-type systems. The spectra exhibited a great number of signals of mono- and bimetallic oligomeric chloride subnanoclusters. Few oligometallic ions had core-shell structures, according to the computations; the structure of most ions was completely unsymmetric, with bridging Cl ⁻ ligands supporting the oligomeric structures. Born-Oppenheimer molecular dynamics showed that some ions were structurally flexible under the selected conditions. Many considered ions exhibited rich configurational and conformational isomerism. The activation (polarization) of the N ₂ molecule (from the drying gas used during electrospray ionization) by some ions was determined by the analysis of electron density distributions. For the first time, we describe a flexible approach for semiautomatic analysis of highly complex mass-spectra of organometallic systems in solution with the possibility of revealing molecular structures.