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. ORCID: 0000-0002-3860-7532, Dolezal, N., Drijfhout, J.W., Wuhrer, M. and Van Der Burgt, Y.E.M., 2020. Evaluation of sibling and twin fragment ions improves the structural characterization of proteins by top-down MALDI in-source decay mass spectrometry. Analytical Chemistry, 92 (8), pp. 5871-5881. ISSN 0003-2700

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Abstract

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.

Item Type: Journal article
Publication Title: Analytical Chemistry
Creators: Nicolardi, S., Kilgour, D.P.A., Dolezal, N., Drijfhout, J.W., Wuhrer, M. and Van Der Burgt, Y.E.M.
Publisher: American Chemical Society
Date: 21 April 2020
Volume: 92
Number: 8
ISSN: 0003-2700
Identifiers:
NumberType
10.1021/acs.analchem.9b05683DOI
1312401Other
Divisions: Schools > School of Science and Technology
Record created by: Jonathan Gallacher
Date Added: 30 Mar 2020 15:48
Last Modified: 26 Jun 2020 09:17
URI: http://irep.ntu.ac.uk/id/eprint/39518

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