TY - JOUR
T1 - An enhanced protein crosslink identification strategy using CID-cleavable chemical crosslinkers and LC/MS n analysis
AU - Liu, Fan
AU - Wu, Cong
AU - Sweedler, Jonathan V.
AU - Goshe, Michael B.
PY - 2012/2
Y1 - 2012/2
N2 - We describe a novel two-step LC/MS n strategy to effectively and confidently identify numerous crosslinked peptides from complex mixtures. This method incorporates the use of our gas-phase cleavable crosslinking reagent, disuccinimidyl-succinamyl-aspartyl-proline (SuDP), and a new data-processing algorithm CXLinkS (Cleavable Crosslink Selection), which enables unequivocal crosslink peptide selection and identification on the basis of mass measurement accuracy, high resolving power, and the unique fragmentation pattern of each crosslinked peptide. We demonstrate our approach with well-characterized monomeric and multimeric protein systems with and without database searching restrictions where inter-peptide crosslink identification is increased 8-fold over our previously published data-dependent LC/MS 3 method and discuss its applicability to other CID-cleavable crosslinkers and more complex protein systems.
AB - We describe a novel two-step LC/MS n strategy to effectively and confidently identify numerous crosslinked peptides from complex mixtures. This method incorporates the use of our gas-phase cleavable crosslinking reagent, disuccinimidyl-succinamyl-aspartyl-proline (SuDP), and a new data-processing algorithm CXLinkS (Cleavable Crosslink Selection), which enables unequivocal crosslink peptide selection and identification on the basis of mass measurement accuracy, high resolving power, and the unique fragmentation pattern of each crosslinked peptide. We demonstrate our approach with well-characterized monomeric and multimeric protein systems with and without database searching restrictions where inter-peptide crosslink identification is increased 8-fold over our previously published data-dependent LC/MS 3 method and discuss its applicability to other CID-cleavable crosslinkers and more complex protein systems.
KW - CID-cleavable crosslinker
KW - Crosslinking
KW - Mass measurement accuracy
KW - Multistage CID
KW - Protein-protein interactions
KW - Technology
UR - http://www.scopus.com/inward/record.url?scp=84863055703&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84863055703&partnerID=8YFLogxK
U2 - 10.1002/pmic.201100352
DO - 10.1002/pmic.201100352
M3 - Comment/debate
C2 - 22213719
AN - SCOPUS:84863055703
SN - 1615-9853
VL - 12
SP - 401
EP - 405
JO - Proteomics
JF - Proteomics
IS - 3
ER -