RESUMO
We describe the synthesis of two tetrachloroindate ionic liquids used as probes to study the involvement of NHCs (N-heterocyclic carbenes) in the distillation of imidazolium derivatives. Atmospheric-pressure chemical ionization mass spectrometry (APCI-MS), electrospray ionization mass spectrometry (ESI-MS), atmospheric-pressure thermal desorption ion mass spectrometry (APTDI-MS) and laser-induced acoustic desorption (LIAD) were used to depict the possibility of the involvement of NHCs during the distillation process. Each type of imidazolium derivative showed a particular mechanism of distillation, pointing firmly to the dependence of both the cation and the anion natures to distil as ion pairs or NHCs. Ionic liquid 1-n-butyl-3-methylimidazolium tetrachloroindate (1a) exhibited a preference to distil as ion pairs, whereas 3,3'-(ethane-1,2-diyl)bis(1-methyimidazolium)bis-tetrachloroindate (1b) may react with the Lewis acid anion, affording a bidentate NHC complex to distil. Thermodynamics, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses of the ionic liquid 1a were also conducted and helped understand the preference for ion pairs instead of NHCs. The performed theoretical calculations did not forwent the possibility of NHC formation; however, they clearly indicated the high stability of the anions (Lewis acids in nature) and also indicated that the possible reaction between NHC and the anion is not favoured. The calculated thermodynamic values were in accordance with the features observed by MS and indicated ion pairs as the feasible species for the distillation of imidazolium-based ionic liquids.
RESUMO
Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677). This article is part of a Special Issue entitled: Computational Proteomics.