Targeted Annotation of S‑Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry

Protein S-sulfinylation (R–SO₂^–) and S-sulfonylation (R–SO₃^–) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site

Designing Efficient Localized Surface Plasmon Resonance-Based Sensing Platforms: Optimization of Sensor Response by Controlling the Edge Length of Gold Nanoprisms

Over the past few years, the unique localized surface plasmon resonance properties of plasmonic nanostructures have been used to design label-free biosensors. In this article, we demonstrate that it is the difference in edge length of gold nanoprisms that significantly influences their bulk refractive index sensitivity and local sensing efficiency. Nanoprisms with edge lengths in the range of 28–51 nm were synthesized by the chemical-reduction method and sensing platforms were fabricated by chemisorption of these nanoprisms onto silanized glass substrates. The plasmonic nanosensors fabricated from 28 nm edge length nanoprisms exhibited the largest sensitivity to change in bulk refractive index with a value of 647 nm/RIU. The refractive index sensitivity decreased with increasing edge length, with nanoprisms of 51 nm edge length, displaying a sensitivity of 384 nm/RIU. In contrast, we found that the biosensing efficiency of sensing platforms modified with biotin increased with increasing edge length, with sensing platforms fabricated from 51 nm edge length nanoprisms displaying the highest local sensing efficiency. The lowest concentration of streptavidin that could be measured reliably with this edge length nanoprism was 1.0 pM and the limit of detection was 0.5 pM, which is much lower than found with gold bipyramids, nanostars, and nanorods. In addition, the electromagnetic-field decay length of the sensing platforms was substantially influenced by the edge-length of the nanoprisms