We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein-interaction studies.

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, 15 N 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.

Abstract. Discerning mechanisms of sulfate formation during fine-particle pollution (referred to as haze hereafter) in Beijing is important for understanding the rapid evolution of haze and for developing cost-effective air pollution mitigation strategies. Here we present observations of the oxygen-17 excess of PM 2.5 sulfate ( 17 O(SO 2− 4 )) collected in Beijing haze from October 2014 to January 2015 to constrain possible sulfate formation pathways. Throughout the sampling campaign, the 12-hourly averaged PM 2.5 concentrations ranged from 16 to 323 µg m −3 with a mean of (141 ± 88 (1σ )) µg m −3 , with SO Our estimate suggested that in-cloud reactions dominated sulfate production on polluted days (PDs, PM 2.5 ≥ 75 µg m −3 ) of Case II in October 2014 due to the relatively high cloud liquid water content, with a fractional contribution of up to 68 %. During PDs of Cases I and III-V, heterogeneous sulfate production (P het ) was estimated to contribute 41-54 % to total sulfate formation with a mean of (48 ± 5) %. For the specific mechanisms of heterogeneous oxidation of SO 2 , chemical reaction kinetics calculations suggested S(IV) (= SO 2 q H 2 O + HSO − 3 + SO 2− 3 ) oxidation by H 2 O 2 in aerosol water accounted for 5-13 % of P het . The relative importance of heterogeneous sulfate production by other mechanisms was constrained by our observed 17 O(SO 2− 4 ). Heterogeneous sulfate production via S(IV) oxidation by O 3 was estimated to contribute 21-22 % of P het on average. Heterogeneous sulfate production pathways that result in zero-17 O(SO 2− 4 ), such as S(IV) oxidation by NO 2 in aerosol water and/or by O 2 via a radical chain mechanism, contributed the remaining 66-73 % of P het . The assumption about the thermodynamic state of aerosols (stable or metastable) was found to significantly influence the calculated aerosol pH (7.6 ± 0.1 or 4.7 ± 1.1, respectively), and thus influence the relative importance of heterogeneous sulfate production via S(IV) oxidation by NO 2 and by O 2 . Our local atmospheric conditions-based calculations suggest sulfate formation via NO 2 oxidation can be the dominant pathway in aerosols at high-pH conditions calculated assuming stable state while S(IV) oxidation by O 2 can be the dominant pathway providing that highly acidic aerosols (pH ≤ 3) exist. Our local atmospheric-conditions-based calculations illustrate the utility of 17 O(SO 2− 4 ) for quantifying sulfate forPublished by Copernicus Publications on behalf of the European Geosciences Union. 5516 P. He et al.: Isotopic constraints on heterogeneous sulfate production in Beijing haze mation pathways, but this estimate may be further improved with future regional modeling work.

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.