Journal
ANALYTICAL CHEMISTRY
Volume 78, Issue 7, Pages 2145-2149Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ac051339c
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Funding
- NCRR NIH HHS [1S10RR17262-01] Funding Source: Medline
- NIAID NIH HHS [1U54AI57141-01] Funding Source: Medline
- NIEHS NIH HHS [P30ES07033] Funding Source: Medline
- NIGMS NIH HHS [GM32165] Funding Source: Medline
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To facilitate structural analysis of proteins and protein-protein interactions, we developed Pro-CrossUnk, a suite of software tools consisting of three programs (Figure 1), DetectShift, ldentifyXUnk, and AssignXLink. DetectShift was developed to detect ions of cross-linked peptide pairs in a mixture of O-18-labeled peptides obtained from protein proteolytic digests. The selected candidate ions of crosslinked peptide pairs subsequently undergo tandem mass spectrometric (MS/MS) analysis for sequence determination. Based on the masses of candidate ions as well as y- and b-type ions in the tandem mass spectra, IdentifyX-Link assigns the candidate ions to cross-linked peptide pairs. For an identified cross-linked peptide pair, AssignXLink generates an extensive fragment ion list, including a-, b-, c-type, x-, Y-9 Z-type, internal, and immonium ions with associated common losses of H2O, NH3, CO, and CO2, and facilitates a precise location of the cross-linked residues. Pro-CrossUnk is automated, highly configurable by the user, and applicable to many studies that map low-resolution protein structures and molecular interfaces in protein complexes.
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