Evaluating the Performance of 193 nm Ultraviolet Photodissociation for Tandem Mass Tag Labeled Peptides

Despite the successful application of tandem mass tags (TMT) for peptide quantitation, missing reporter ions in higher energy collisional dissociation (HCD) spectra remains a challenge for consistent quantitation, especially for peptides with labile post-translational modifications. Ultraviolet photodissociation (UVPD) is an alternative ion activation method shown to provide superior coverage for sequencing of peptides and intact proteins. Here, we optimized and evaluated 193 nm UVPD for the characterization of TMT-labeled model peptides, HeLa proteome, and N-glycopeptides from model proteins. UVPD yielded the same TMT reporter ions as HCD, at m/z 126–131. Additionally, UVPD produced a wide range of fragments that yielded more complete characterization of glycopeptides and less frequent missing TMT reporter ion channels, whereas HCD yielded a strong tradeoff between characterization and quantitation of TMT-labeled glycopeptides. However, the lower fragmentation efficiency of UVPD yielded fewer peptide identifications than HCD. Overall, 193 nm UVPD is a valuable tool that provides an alternative to HCD for the quantitation of large and highly modified peptides with labile PTMs. Continued development of instrumentation specific to UVPD will yield greater fragmentation efficiency and fulfil the potential of UVPD to be an all-in-one spectrum ion activation method for broad use in the field of proteomics.

Proteomics reveals that quinoa bioester promotes replenishing effects in epidermal tissue

The continuous search for natural products that attenuate age-related losses has increasingly gained notice; among them, those applicable for skin care have drawn significant attention. The bioester generated from the Chenopodium quinoa’s oil is a natural-origin ingredient described to produce replenishing skin effects. With this as motivation, we used shotgun proteomics to study the effects of quinoa bioester on human reconstructed epidermis tridimensional cell cultures after 0, 3, 6, 12, 24, and 48 h of exposure. Our experimental setup employed reversed-phase nano-chromatography coupled online with an Orbitrap-XL and PatternLab for proteomics as the data analysis tool. Extracted ion chromatograms were obtained as surrogates for relative peptide quantitation. Our findings spotlight proteins with increased abundance, as compared to the untreated cell culture counterparts at the same timepoints, that were related to preventing premature aging, homeostasis, tissue regeneration, protection against ultraviolet radiation and oxidative damage.

Development of a UPLC-IDA-ICP-MS/MS method for peptide quantitation in plasma by Se-labelling, and comparison to S-detection of the native peptide

Se-labelling improves quantitation of peptides in plasma significantly compared to S-detection of the native peptide.