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Updated: Jan 17, 2026

Analyzing Large Protein Complexes by Structural Mass Spectrometry
Published on: June 19, 2010
Mass-Invariant Natural Log-Transformed Mass Spectra Enable Internal Calibration and De Novo Sequencing of Intact
Lissa C Anderson1,2, Nathan K Kaiser1, Krishna Saketh Kamadana3
1National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States.
Abstract:
A key limitation of top-down proteomics is reliance on averagine-based deconvolution to estimate monoisotopic masses, which introduces systematic errors when isotope envelopes are distorted. We present a framework that bypasses averagine by operating directly in natural log-transformed m/z space, where charge-state spacing is mass-invariant and provides an intrinsic reference for internal calibration on both FT-ICR and Orbitrap analyzers. Isotopologue pairing in this domain supports de novo sequencing and discriminates near-isobaric residues. By shifting the paradigm from monoisotopic mass estimation to connectivity-driven inference, the approach offers resilience against distorted isotope envelopes and unknown PTMs, establishing a database-independent strategy for discovery-oriented proteoform characterization without known calibrants.
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