A Negative Ion Mass Spectrometry Approach to Identify Cross-Linked Peptides Utilizing Characteristic Disulfide Fragmentations

A N Calabrese; N J Good; Tianfang Wang; J He; J H Bowie; T L Pukala

doi:10.1007/s13361-012-0407-x

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A Negative Ion Mass Spectrometry Approach to Identify Cross-Linked Peptides Utilizing Characteristic Disulfide Fragmentations

Journal article

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A Negative Ion Mass Spectrometry Approach to Identify Cross-Linked Peptides Utilizing Characteristic Disulfide Fragmentations

A N Calabrese, N J Good, Tianfang Wang, J He, J H Bowie and T L Pukala

Journal of The American Society for Mass Spectrometry, Vol.23(8), pp.1364-1375

2012

DOI: https://doi.org/10.1007/s13361-012-0407-x

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Abstract

negative ion mass spectrometry

chemical cross-linking

disulfide fragmentations

protein structure determination

Chemical cross-linking combined with mass spectrometry (MS) is an analytical tool used to elucidate the topologies of proteins and protein complexes. However, identification of the low abundance cross-linked peptides and modification sites amongst a large quantity of proteolytic fragments remains challenging. In this work, we present a strategy to identify cross-linked peptides by negative ion MS for the first time. This approach is based around the facile cleavages of disulfide bonds in the negative mode, and allows identification of cross-linked products based on their characteristic fragmentations. MS3 analysis of the cross-linked peptides allows for their sequencing and identification, with residue specific location of cross-linking sites. We demonstrate the applicability of the commercially available cystine based cross-linking reagent dithiobis(succinimidyl) propionate (DSP) and identify cross-linked peptides from ubiquitin. In each instance, the characteristic fragmentation behavior of the cross-linked species is described. The data presented here indicate that this negative ion approach may be a useful tool to characterize the structures of proteins and protein complexes, and provides the basis for the development of high throughput negative ion MS chemical cross-linking strategies.

Details

Title: A Negative Ion Mass Spectrometry Approach to Identify Cross-Linked Peptides Utilizing Characteristic Disulfide Fragmentations
Authors: A N Calabrese (Author) - University of Adelaide
N J Good (Author) - University of Adelaide
Tianfang Wang (Author) - University of Adelaide
J He (Author) - University of Adelaide
J H Bowie (Author) - University of Adelaide
T L Pukala (Author) - University of Adelaide
Publication details: Journal of The American Society for Mass Spectrometry, Vol.23(8), pp.1364-1375
Publisher: Springer New York LLC
Date published: 2012
DOI: 10.1007/s13361-012-0407-x
ISSN: 1044-0305
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99450279102621
Output Type: Journal article

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