Abstract
Development of new reagents for protein cross-linking is constantly ongoing. The chemical formulas for the linker adducts formed by these reagents are usually deduced from expert knowledge and then validated by mass spectrometry. Clearly, it would be more rigorous to infer the chemical compositions of the adducts directly from the data without any prior assumptions on their chemistries. Unfortunately, the analysis tools that are currently available to detect chemical modifications on linear peptides are not applicable to the case of two cross-linked peptides. Here, we show that an adaptation of the open search strategy that works on linear peptides can be used to characterize cross-link modifications in pairs of peptides. We benchmark our approach by correctly inferring the linker masses of two well-known reagents, DSS and formaldehyde, to accuracies of a few parts per million. We then investigate the cross-linking chemistries of two poorly characterized reagents: EMCS and glutaraldehyde. In the case of EMCS, we find that the expected cross-linking chemistry is accompanied by a competing chemistry that targets other amino acid types. In the case of glutaraldehyde, we find that the chemical formula of the dominant linker is C5H4, which indicates a ringed aromatic structure. These results demonstrate how, with very little effort, our approach can yield nontrivial insights to better characterize new cross-linkers.
Highlights
Mass spectrometry is the main tool for the discovery and characterization of new types of protein modifications.[1]
The mass spectrometry measurements provide two data-dependent MS/MS data sets that are the inputs for the computational analysis
Ammonium bicarbonate was shown to enhance the formation of hydrolyzed species,[26] and is probably the causative agent in our samples. All of these findings demonstrate that the actual EMCS linking chemistry is rather different from the one predicted, highlighting the importance of an unbiased open search
Summary
Mass spectrometry is the main tool for the discovery and characterization of new types of protein modifications.[1] In peptide digests of protein mixtures, modifications manifest as unexplained differences between the measured and theoretical masses of certain peptides. For novel modifications, these mass differences are not known a priori and, it is not straightforward to infer them from the data. At the level of the peptide digest, a cross-link modification manifests as a pair of peptides connected by a linker adduct. In XL-MS, intact proteins are reacted with a bifunctional cross-linking reagent that creates stable covalent links between side chains that are spatially close to each other
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