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2016 ; 88
(20
): 10301-10308
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Developing a Multiplexed Quantitative Cross-Linking Mass Spectrometry Platform
for Comparative Structural Analysis of Protein Complexes
#MMPMID27626298
Yu C
; Huszagh A
; Viner R
; Novitsky EJ
; Rychnovsky SD
; Huang L
Anal Chem
2016[Oct]; 88
(20
): 10301-10308
PMID27626298
show ga
Cross-linking mass spectrometry (XL-MS) represents a recently popularized hybrid
methodology for defining protein-protein interactions (PPIs) and analyzing
structures of large protein assemblies. In particular, XL-MS strategies have been
demonstrated to be effective in elucidating molecular details of PPIs at the
peptide resolution, providing a complementary set of structural data that can be
utilized to refine existing complex structures or direct de novo modeling of
unknown protein structures. To study structural and interaction dynamics of
protein complexes, quantitative cross-linking mass spectrometry (QXL-MS)
strategies based on isotope-labeled cross-linkers have been developed. Although
successful, these approaches are mostly limited to pairwise comparisons. In order
to establish a robust workflow enabling comparative analysis of multiple
cross-linked samples simultaneously, we have developed a multiplexed QXL-MS
strategy, namely, QMIX (Quantitation of Multiplexed, Isobaric-labeled cross
(X)-linked peptides) by integrating MS-cleavable cross-linkers with isobaric
labeling reagents. This study has established a new analytical platform for
quantitative analysis of cross-linked peptides, which can be directly applied for
multiplexed comparisons of the conformational dynamics of protein complexes and
PPIs at the proteome scale in future studies.