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Surface-Induced Dissociation of Anionic vs Cationic Native-Like Protein Complexes.

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Negative mode native mass spectrometry (nMS) provides structural insights into protein complexes. This method offers charge reduction without peak broadening, revealing substructural details of complexes like the human proteasome.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Structural Biology

Background:

  • Understanding protein complex assembly is crucial for biological function.
  • Native mass spectrometry (nMS) is a powerful technique for studying protein complexes.
  • Traditional positive mode nMS often requires charge reduction, which can lead to peak broadening.

Purpose of the Study:

  • To investigate the utility of negative mode ionization in nMS for studying protein complex structure.
  • To demonstrate that negative mode nMS coupled with surface-induced dissociation (SID) provides substructural information.
  • To highlight the advantages of negative mode ionization over positive mode for charge reduction.

Main Methods:

  • Utilizing negative mode ionization in nMS with ammonium acetate.
  • Applying surface-induced dissociation (SID) to fragment protein complex anions.
  • Analyzing the fragmentation patterns of the 20S human proteasome.

Main Results:

  • Negative mode ionization yields lower charge states for protein complexes compared to positive mode.
  • Fragmenting protein complex anions via SID provides substructural information consistent with solved structures.
  • Negative mode nMS/SID avoids the peak broadening associated with solution phase charge reduction additives.
  • The 20S human proteasome was fragmented to reveal subunit connectivity and proteoform information.

Conclusions:

  • Negative mode nMS coupled with SID is an effective method for obtaining substructural information on protein complexes.
  • This approach offers advantages over traditional positive mode nMS, particularly in charge reduction and structural detail.
  • Negative mode nMS/SID provides valuable insights into the architecture and heterogeneity of large protein assemblies.