Evaluation of sibling and twin fragment ions improves the structural characterization of proteins by top-down MALDI in-source decay mass spectrometry

Nicolardi, S.; Kilgour, D.P.A.; Dolezal, N.; Drijfhout, J.W.; Wuhrer, M.; Burgt, Y.E.M. van der (2020)

Article / Letter to editor

Comprehensive determination of primary sequence and identification of post-translational modifications (PTMs) are key elements in protein structural analysis. Various mass spectrometry (MS) based fragmentation techniques are powerful approaches for mapping both the amino acid sequence and PTMs; one of these techniques is matrix-assisted laser desorption/ionization (MALDI), combined with in-source decay (ISD) fragmentation and Fourier-transform ion cyclotron resonance (FT-ICR) MS. MALDI-ISD MS protein analysis involves only minimal sample preparation and does not require spectral deconvolution. The resulting MALDI-ISD MS data is complementary to electrospray ionization-based MS/MS sequencing readouts, providing knowledge on the types of fragment ions is available. In this study, we evaluate the isotopic distributions of z' ions in protein top-down MALDI-ISD FT-ICR mass spectra and show why these distributions can deviate from theoretical profiles as a result of co-occurring and isomeric z and y-NH3 ions. Two synthetic peptides, containing either normal or deuterated alanine residues, were used to confirm the presence and unravel the identity of isomeric z and y-NH3 fragment ions ("twins"). Furthermore, two reducing MALDI matrices, namely 1,5-diaminonaphthalene and N-phenyl-p-phenylenediamine were applied that yield ISD mass spectra with different fragment ion distributions. This study demonstrates that the relative abundance of isomeric z and y-NH3 ions requires consideration for accurate and confident assignments of z' ions in MALDI-ISD FT-ICR mass spectra.

• All authors: Nicolardi, S.; Kilgour, D.P.A.; Dolezal, N.; Drijfhout, J.W.; Wuhrer, M.; Burgt, Y.E.M. van der
• Date: 2020-04-21
• Journal: Analytical Chemistry
• Volume: 92
• Issue: 8
• Pages: 5871 - 5881
• DOI: doi:10.1021/acs.analchem.9b05683
• Link: https://pubs.acs.org/doi/10.1021/acs.analchem.9b05683