Dataset Information

Improving Mass Spectrometry Analysis of Protein Structures with Arginine-Selective Chemical Cross-linkers

ABSTRACT: we develop a series of arginine selective bifunctional aromatic glyoxal cross-linkers (ArGOs) and demonstrate their ability to cross-link model proteins and a protein complex. We also introduce the first arginine-lysine heterobifunctional cross-linker (KArGO), which provides significantly greater surface coverage than the corresponding homobifunctional reagents (e.g. ArGOs and BS3), due to access to the combined abundances of lysine and arginine residues.

ORGANISM(S): Escherichia Coli

SUBMITTER: Meng-Qiu Dong

PROVIDER: PXD012341 | iProX | Mon Jan 14 00:00:00 GMT 2019

REPOSITORIES: iProX

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Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers.

Jones Alexander X AX Cao Yong Y Tang Yu-Liang YL Wang Jian-Hua JH Ding Yue-He YH Tan Hui H Chen Zhen-Lin ZL Fang Run-Qian RQ Yin Jili J Chen Rong-Chang RC Zhu Xing X She Yang Y Huang Niu N Shao Feng F Ye Keqiong K Sun Rui-Xiang RX He Si-Min SM Lei Xiaoguang X Dong Meng-Qiu MQ

Nature communications 20190902 1

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine ...[more]

PMID: 31477730

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Project description:Numerous reagents have been developed to enable chemical proteomic analysis of small molecule-protein interactomes. However, the performance of these reagents has not been systematically evaluated and compared. Herein, we report our efforts to conduct a parallel assessment of two widely-used chemically-cleavable linkers equipped with dialkoxydiphenylsilane (DADPS linker) and azobenzene (AZO linker) moieties. Profiling a cellular cysteinome using iodoacetamide alkyne probe demonstrated a significant discrepancy between the experimental results obtained through the application of each of the reagents. To better understand the source of observed discrepancy, a mass tolerant database search strategy using MSFragger software was performed. This resulted in identifying a previously unreported artifactual modification on the residual mass of the azobenzene linker. Furthermore, we conducted a comparative analysis of enrichment modes using both cleavable linkers. This effort determined that enrichment of proteolytic digests yielded a far greater number of identified cysteine residues than the enrichment conducted prior to protein digest. Inspired by recent studies where multiplexed quantitative labeling strategies were applied to cleavable biotin linkers, we combined this further optimized protocol using the DADPS cleavable linker with tandem mass tag (TMT) labeling to profile the FDA-approved covalent EGFR kinase inhibitor dacomitinib against the cysteinome of an epidermoid cancer cell line. Our analysis resulted in the detection and quantification of over 10,000 unique cysteine residues, a nearly 3-fold increase over previous studies that used cleavable biotin linkers for enrichment. Critically, cysteine residues corresponding to proteins directly as well as indirectly modulated by dacomitinib treatment were identified. Overall, our study suggests that the dialkoxydiphenylsilane linker could be broadly applied wherever chemically cleavable linkers are required for chemical proteomic characterization of cellular proteomes.

Dataset Information

Improving Mass Spectrometry Analysis of Protein Structures with Arginine-Selective Chemical Cross-linkers

Publications

Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers.

Similar Datasets

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