Mass-Invariant Natural Log-Transformed Mass Spectra Enable Internal Calibration and De Novo Sequencing of Intact Proteins
peer-reviewed · Analytical Chemistry · 2026
| Date | 2026-01-27 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1021/acs.analchem.5c06165 |
| Citations (OpenAlex) | 0 |
| Venue 2-year citedness | 7.10 |
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.
Methods and tools
- Log-transformed mass domain de novo sequencing: Bypasses averagine-based deconvolution by working directly in natural log-transformed m/z space, where charge-state spacing is mass-invariant and therefore supplies an intrinsic internal-calibration reference on both FT-ICR and Orbitrap. Isotopologue pairing in that domain then supports de novo sequencing of intact proteins.