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

Abstract

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.

Advanced tandem mass spectrometry in metabolomics and lipidomics—methods and applications

“…IRMPD tandem MS allowed to obtain structurally diagnostic fragment ions suggesting that S=O groups efficiently absorb 10.6 μm photons. This is also consistent with the recent observation that Ssulfonylated peptides readily fragment upon IRMPD [62]. In other studies of plant metabolites that lacked functional groups that efficiently absorb 10.6 μm IR radiation, IRMPD and CID fragment ions and fragment ion intensities were similar [63].…”

Unbiased Detection of Cysteine Sulfenic Acid by 473 nm Photodissociation Mass Spectrometry: Toward Facile In Vivo Oxidative Status of Plasma Proteins

“…The added value of the exquisite fragmentation specificity provided by laser-induced dissociation (LID) to detect a peptide subpopulation has been highlighted many times, for instance, with infrared multiphoton photodissociation at 10.6 μm for targeting sulfonated peptides. , Intrinsic chromophores such as disulfide bonds or tyrosine residues have been similarly used for specific detection in the ultraviolet range (UVPD). , The grafting of amino-acid side chains with a proper chromophore is an alternative for introducing specificity at the fragmentation step. With the aim of targeting a Cys-containing peptide, this concept has been implemented using the judicious selection of chromophores absorbing in the UV range at 351 and 266 nm , or in the visible range at 473 nm. − …”

Increasing specificity of tandem mass spectrometry by laser‐induced dissociation

“…As an illustration, infrared multiphoton photodissociation (IRMPD) at 10.6 μm has shown the interesting propensity to differentiate phospho‐ and non‐phosphorylated peptides due to the increased photon absorption of the phosphate group. Moreover, IRMPD shows specificity towards sulfonated peptides . LID in the UV range (UVPD at 266 nm) also offers excellent versatility because the absorption of native biomolecules depends on their intrinsic chromophores such as disulfide bound or tyrosine, tryptophan and phenylalanine residues .…”

“…Moreover, IRMPD shows specificity towards sulfonated peptides. 11,12 LID in the UV range (UVPD at 266 nm) also offers excellent versatility because the absorption of native biomolecules depends on their intrinsic chromophores such as disulfide bound or tyrosine, tryptophan and phenylalanine residues. [13][14][15] However, the most obvious strategy for incorporating a higher degree of fragmentation specificity into a proteomics workflow is to target only a subset of peptides after derivatization with specific chromophores in the visible range.…”