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Updated: Oct 26, 2026

Analyzing Large Protein Complexes by Structural Mass Spectrometry
Published on: June 19, 2010
A Tutorial on Automated Mass Spectral Analysis Using NucleoSpec for Compositional Assignment of Nucleic Acid-Silver
I-Hsin Lin1, Stacy M Copp1,2,3,4
1Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States.
Abstract:
Nucleic acid-metal complexes, such as DNA-stabilized silver nanoclusters (DNA-Ag N ) and Ag-(I)-mediated DNA duplexes, show promise for applications ranging from biomedical imaging to bioelectronics and sensing. Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool for precisely resolving their compositions, but the data analysis procedure can be challenging and time-consuming. No general-purpose software can automatically assign compositions of nucleic acid-silver complexes, most notably for DNA-Ag N , whose masses depend on the oxidation state of the silver core. We address these challenges by developing an automated data analysis workflow for ESI-MS of nucleic acid-silver complexes. This tutorial presents the analysis workflow and introduces NucleoSpec, an open-source, web-based platform that consolidates charge state determination, constraint-based composition enumeration, isotope-pattern matching, and adduct/conjugate handling into a single browser-accessible interface. The platform is benchmarked on published molecular formulas determined by manual analysis for DNA-Ag N , xeno-nucleic acid stabilized Ag N (XNA-Ag N ), nucleic acid-Ag-(I) complexes, and chemically modified DNA-Ag N , reproducing assignments to single-proton precision (median centroid offset of 0.03 m/z) for spectra of adequate signal-to-noise. Low-signal peaks for which adjacent valence electron counts become difficult to distinguish are flagged by NucleoSpec for user inspection. By lowering the barrier to high-resolution compositional analysis and supporting integration into high-throughput pipelines, NucleoSpec addresses a key experimental bottleneck in informatics-guided design of nucleic acid-metal complexes.
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