Compelling Advantages of Negative Ion Mode Detection in High-Mass MALDI-MS for Homomeric Protein Complexes

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Author(s) Mädler, Stefanie, Barylyuk, Konstantin, Erba, Elisabetta Boeri, Nieckarz, Robert J., Zenobi, Renato
Publication Type Journal Items, Publication Status: Published
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Title Compelling Advantages of Negative Ion Mode Detection in High-Mass MALDI-MS for Homomeric Protein Complexes
Author(s) Mädler, Stefanie
Barylyuk, Konstantin
Erba, Elisabetta Boeri
Nieckarz, Robert J.
Zenobi, Renato
Journal or Series Title Journal of the American Society for Mass Spectrometry
Volume Number 23
Issue Number 2
Start Page 213
End Page 224
ISSN 1044-0305
Publisher Springer
Publication Place New York
Publication Date 2012-02
Keyword(s) Chemical cross-linking
NHS ester
Multiply charged ions
Abstract Chemical cross-linking in combination with high-mass MALDI mass spectrometry allows for the rapid identification of interactions and determination of the complex stoichiometry of noncovalent protein-protein interactions. As the molecular weight of these complexes increases, the fraction of multiply charged species typically increases. In the case of homomeric complexes, signals from multiply charged multimers overlap with singly charged subunits. Remarkably, spectra recorded in negative ion mode show lower abundances of multiply charged species, lower background, higher reproducibility, and, thus, overall cleaner spectra compared with positive ion mode spectra. In this work, a dedicated high-mass detector was applied for measuring high-mass proteins (up to 200 kDa) by negative ion mode MALDI-MS. The influences of sample preparation and instrumental parameters were carefully investigated. Relative signal integrals of multiply charged anions were relatively independent of any of the examined parameters and could thus be approximated easily for the spectra of cross-linked complexes. For example, the fraction of doubly charged anions signals overlapping with the signals of singly charged subunits could be more precisely estimated than in positive ion mode. Sinapinic acid was found to be an excellent matrix for the analysis of proteins and cross-linked protein complexes in both ion modes. Our results suggest that negative ion mode data of chemically cross-linked protein complexes are complementary to positive ion mode data and can in some cases represent the solution phase situation better than positive ion mode.
DOI 10.1007/s13361-011-0274-x
Additional Notes Received 5 August 2011, Revised 4 October 2011, Accepted 8 October 2011, Published online 1 December 2011
Document Type Article
Publication Status Published
Language English
NEBIS System Number 000541631
Source Database ID WOS-000302467800003
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  author = "M{\"{a}}dler, Stefanie and Barylyuk, Konstantin and Erba, Elisabetta Boeri and Nieckarz, Robert J. and Zenobi, Renato",
  title = "{C}ompelling {A}dvantages of {N}egative {I}on {M}ode {D}etection in {H}igh-{M}ass {M}{A}{L}{D}{I}-{M}{S} for {H}omomeric {P}rotein {C}omplexes",
  journal = "Journal of the American Society for Mass Spectrometry",
  year = 2012,
  volume = "23",
  number = "2",
  pages = "213--224",
  month = feb,

E-Citations record created: Mon, 07 May 2012, 10:05:15 CET