Mapping native disulfide bonds at a proteome scale.

We developed a high-throughput mass spectrometry method, pLink-SS (http://pfind.ict.ac.cn/software/pLink/2014/pLink-SS.html), for precise identification of disulfide-linked peptides. Using pLink-SS, we mapped all native disulfide bonds of a monoclonal antibody and ten standard proteins. We performed disulfide proteome analyses and identified 199 disulfide bonds in Escherichia coli and 568 in proteins secreted by human endothelial cells. We discovered many regulatory disulfide bonds involving catalytic or metal-binding cysteine residues.

Facile Fabrication of Highly Stable and Wavelength-Tunable Tin Based Perovskite Materials with Enhanced Quantum Yield via the Cation Transformation Reaction.

Metal halide perovskites have attracted great attention for their superior light energy conversion applications. Herein, we demonstrated a facile synthesis of zero-dimensional Sn2+ perovskite Cs4-xMxSnBr6(M = K+ and Rb+) material through the cation transformation reaction at room temperature. Cs4SnBr6 NCs was mixed with pure metal bromide salts (KBr and RbBr) via the mechanochemical process to successfully synthesize Cs4-xMxSnBr6 perovskite where transformation of Cs to mixed Cs/Rb and mixed Cs/K was achieved. By substituting different cations, the bright fluorescence of the Cs4-xMxSnBr6 was tuned from dim green to greenish-cyan while achieving the photoluminescence (PL) quantum yield of ∼39%. The crystal structure of Sn based perovskite with the substitution of K+ or Rb+ cations was determined by X-ray diffraction (XRD). Moreover, the Cs4-xMxSnBr6 demonstrated superior air stability and exhibited a better photocatalytic activity for CO2 reduction reaction (CO2RR) with high selectivity of CH4 gas with a higher yield rate compared to the pristine Cs4SnBr6 NCs.

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides.

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.

Using pLink to Analyze Cross-Linked Peptides.

pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink.