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TitleIsotope Decluttering Reduces Spectral Complexity while Maintaining Protein Structure.
Journal, issue, pagesAnal Chem, Vol. 98, Issue 22, Page 16063-16072, Year 2026
Publish dateJun 9, 2026
AuthorsSneha S Hakke / Willem E M Noteborn / Birol Cabukusta / Ye Gao / Kèvin Knoops / Carmen López-Iglesias / David P A Kilgour / David J Clarke / Anjusha Mathew / Ron M A Heeren /
PubMed AbstractAccurate mass determination is one of the fundamental objectives in mass spectrometry (MS) as it enables confident molecular identification and detection of subtle mass differences. Precise mass ...Accurate mass determination is one of the fundamental objectives in mass spectrometry (MS) as it enables confident molecular identification and detection of subtle mass differences. Precise mass determination typically relies on the measurement of the monoisotopic peak. The increasing number of heavier isotopes, as the molecular mass increases, leads to spectral complexity, broadening of the isotopic distribution, and dispersal of signal intensity, ultimately reducing the signal-to-noise ratio (SNR). These effects are enhanced while analyzing larger proteins and protein complexes. In this study, we expressed and purified two protein complexes, EsxAB and bacterioferritin B (BfrB), under isotope-depleted conditions to reduce the abundances of the heavier isotopes of carbon and nitrogen. We applied isotope depletion to BfrB, which represents the largest mass of the isotope-depleted protein complex studied under native conditions to date, and, for the first time, investigated its structural consequences. Isotope-depleted proteins as well as protein complexes showed simplified mass spectra by reducing the isotopic distribution, with a significant increase in the SNR of the monoisotopic peak followed by improved protein sequence coverage by native top-down MS. Furthermore, our investigation of protein structure, by single-particle analysis using cryo-electron microscopy (cryo-EM), demonstrated that isotope depletion preserves the structural integrity of proteins, even at atomic resolution. Collectively, our findings show that isotope depletion is a suitable method for high-accuracy mass measurement and identification by MS while maintaining the structural integrity of the proteins.
External linksAnal Chem / PubMed:42212855 / PubMed Central
MethodsEM (single particle)
Resolution1.79 - 1.8 Å
Structure data

55792

9tcm

EMDB-55792, PDB-9tcm:
1.79 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under natural isotope abundance
Method: EM (single particle) / Resolution: 1.79 Å

55793

9tcn

EMDB-55793, PDB-9tcn:
1.80 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under isotope-depleted abundance
Method: EM (single particle) / Resolution: 1.8 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • mycobacterium tuberculosis h37rv (bacteria)
KeywordsMETAL BINDING PROTEIN / BfrB / Fe storage / C13 and N15 Isotope-depleted

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