The effect of histidine oxidation on the dissociation patterns of peptide ions

Hist-i-fy-a multiple histidine post-translational-modification (PTM) prediction server based on protein sequences using convolution neural network: a case study on mass spectroscopy data

Computational characterization of multiple Histidine (His) post-translational-modifications (PTM) at enzyme active sites complements tedious experimental characterization in proteins-of-unknown-functions (PUFs) and domain-of-unknown-functions (DUFs). There are only a handful of Histidine-PTM-prediction-tools and those also annotate only a single function. Here, we addressed the problem using artificial neural networks on functional histidine dataset curated from enzyme (protein) sequences available in UniProt database (sample size n = 1584). The convolution-neural-network (CNN) model ('Hist-i-fy') performed the best with 75% overall accuracy/F1-score. A case study was performed on histidine-phosphorylation (n = 34) obtained from mass spectroscopy data. For the first time, we report multiple His-PTM-prediction-tool (https://histify.streamlit.app/& https://github.com/dibyansu24-maker/Histify), with optimal performance. The inputs to the tool are (i) protein sequence containing histidine, and (ii) the histidine residue number. Prediction output is one out of the eight histidine functions-acetylation, ribosylation, glycosylation, hydroxylation, methylation, oxidation, phosphorylation, and protein splicing.Communicated by Ramaswamy H. Sarma.

Final Products of One-Electron Oxidation of Cyclic Dipeptides Containing Methionine Investigated by IRMPD Spectroscopy: Does the Free Radical Choose the Final Compound?

Reactive oxygen species (ROS) such as hydrogen peroxide (H₂O₂) and the hydroxyl radical (^•OH) have specific functions in biological processes, while their uncontrolled production and reactivity are known to be determining factors in pathophysiology. Methionine (Met) residues act as endogenous antioxidants, when they are oxidized into methionine sulfoxide (MetSO), thus depleting ROS and protecting the protein. We employed tandem mass spectrometry combined with IR multiple photon dissociation spectroscopy to study the oxidation induced by OH radicals produced by γ radiolysis on model cyclic dipeptides c(LMetLMet), c(LMetDMet), and c(GlyMet). Our aim was to characterize the geometries of the oxidized peptides in the gas phase and to understand the relationship between the structure of the 2-center 3-electron (2c-3e) free radical formed in the first step of the oxidation process and the final compound. Density functional theory calculations were performed to characterize the lowest energy structures of the final product of oxidation and to interpret the IR spectra. Collision-induced dissociation tandem mass spectrometry (CID-MS²) experiments of oxidized c(LMetLMet)H⁺ and c(LMetDMet)H⁺ led to the loss of one or two oxidized sulfenic acid molecules, indicating that the addition of one or two oxygen atoms occurs on the sulfur atom of both methionine side chains and no sulfone formation was observed. The CID-MS² fragmentation mass spectrum of oxidized c(GlyMet)H⁺ showed only the loss of one oxidized sulfenic acid molecule. Thus, the final products of oxidation are the same regardless of the structure of the precursor sulfur-centered free radical.

Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation

Mass spectrometry-based analyses of protein conformation continue to grow in utilization due their speed, low sample requirements, and applicability to most protein systems. These techniques typically rely on chemical derivatization of proteins and as with all label-based analyses must ensure the integrity of the protein conformation throughout the duration of the labeling reaction. Hydroxyl radical footprinting of proteins and the recently developed fast fluoroalkylation of proteins attempt to bypass this consideration via rapid reactions that occur on time scales faster than protein folding, but they often require microfluidic setups or electromagnetic radiation sources. In this work, we demonstrate that ozonation of proteins and peptides, which normally occurs in the second to minute time scales, can be accelerated to the submillisecond to millisecond time scale with an electrospray ionization source. This rapid ozonation results in selective labeling of tryptophan and methionine residues. When applied to cytochrome C and carbonic anhydrase, this labeling technique is sensitive to solution conditions and correlates with solution-phase analyses of conformation. While significant work is still needed to characterize this fast chemical labeling strategy, it requires no complicated sample handling, electromagnetic radiation sources, or microfluidic systems outside of the electrospray source and may represent a facile alternative to other rapid labeling technologies that are utilized today.

Distinguishing Histidine Tautomers in Proteins Using Covalent Labeling-Mass Spectrometry

In this work, we use diethylpyrocarbonate (DEPC)-based covalent labeling together with LC-MS/MS analysis to distinguish the two sidechain tautomers of histidine residues in peptides and proteins. From labeling experiments on model peptides, we demonstrate that DEPC reacts equally with both tautomeric forms to produce chemically different products with distinct dissociation patterns and LC retention times, allowing the ratios of the two tautomers to be determined in peptides and proteins. Upon measuring the tautomer ratios of several histidine residues in myoglobin, we find good agreement with previous 2D NMR data on this protein. Because our DEPC labeling/MS approach is simpler, faster, and more precise than 2D NMR, our method will be a valuable way to determine how protein structure enforces histidine sidechain tautomerization. Because the tautomeric state of histidine residues is often important for protein structure and function, the ability of DEPC labeling/MS to distinguish histidine tautomers should equip researchers with a tool to understand the histidine residue structure and function more deeply in proteins.

Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques

UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.

Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins

Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.

In Vivo Fast Photochemical Oxidation of Proteins Using Enhanced Multiplexing Proteomics

In vivo fast photochemical oxidation of proteins (IV-FPOP) is a hydroxyl radical protein footprinting method used to study protein structure and protein–protein interactions. Oxidatively modified proteins by IV-FPOP are analyzed by mass spectrometry (MS), and the extent of oxidation is quantified by label-free MS. Peptide oxidation changes yield useful information about protein structure, due to changes in solvent accessibility. However, the sample size necessary for animal studies requires increased sample preparation and instrument time. Here, we report the combined application of IV-FPOP and the enhanced multiplexing strategy combined precursor isotopic labeling and isobaric tagging (cPILOT) for higher-throughput analysis of oxidative modifications in C. elegans. Key differences in the performance of label-free MS and cPILOT were identified. The addition of oxygen (+16) was the most abundant modification identified among all known possible FPOP modifications. This study presents IV-FPOP coupled with enhanced multiplexing strategies such as cPILOT to increase throughput of studies seeking to examine oxidative protein modifications.

Role of Buffers in Protein Formulations

Buffers comprise an integral component of protein formulations. Not only do they function to regulate shifts in pH, they also can stabilize proteins by a variety of mechanisms. The ability of buffers to stabilize therapeutic proteins whether in liquid formulations, frozen solutions, or the solid state is highlighted in this review. Addition of buffers can result in increased conformational stability of proteins, whether by ligand binding or by an excluded solute mechanism. In addition, they can alter the colloidal stability of proteins and modulate interfacial damage. Buffers can also lead to destabilization of proteins, and the stability of buffers themselves is presented. Furthermore, the potential safety and toxicity issues of buffers are discussed, with a special emphasis on the influence of buffers on the perceived pain upon injection. Finally, the interaction of buffers with other excipients is examined.

Supercharging by m-NBA Improves ETD-Based Quantification of Hydroxyl Radical Protein Footprinting

Hydroxyl radical protein footprinting (HRPF) is an MS-based technique for analyzing protein structure based on measuring the oxidation of amino acid side chains by hydroxyl radicals diffusing in solution. Spatial resolution of HRPF is limited by the smallest portion of the protein for which oxidation amounts can be accurately quantitated. Previous work has shown electron transfer dissociation (ETD) to be the most reliable method for quantifying the amount of oxidation of each amino acid side chain in a mixture of peptide oxidation isomers, but efficient ETD requires high peptide charge states, which limits its applicability for HRPF. Supercharging reagents have been used to enhance peptide charge state for ETD analysis, but previous work has shown supercharging reagents to enhance charge state differently for different peptides sequences; it is currently unknown if different oxidation isomers will experience different charge enhancement effects. Here, we report the effect of m-nitrobenzyl alcohol (m-NBA) on the ETD-based quantification of peptide oxidation. The addition of m-NBA to both a defined mixture of synthetic isomeric oxidized peptides and Robo-1 protein subjected to HRPF increased the abundance of higher charge state ions, improving our ability to perform efficient ETD of the mixture. No differences in the reported quantitation by ETD were noted in the presence or absence of m-NBA, indicating that all oxidation isomers were charge-enhanced to a similar extent. These results indicate the utility of m-NBA for residue-level quantification of peptide oxidation in HRPF and other applications.

Synthesis of peptides containing 2-oxohistidine residues and their characterization by liquid chromatography-tandem mass spectrometry

Protein oxidation by reactive oxygen species has been associated with aging and neurodegenerative disorders, and histidine is one of the major oxidation targets due to its metal-chelating property and susceptibility to metal-catalyzed oxidation. 2-Oxohistidine, the major product of histidine oxidation, has been recently identified as a stable marker of oxidative damage in biological systems, but its biophysical and biochemical properties are understudied, partly because of difficulties in its chemical synthesis. We developed an efficient method to generate a 2-oxohistidine side chain using metal-catalyzed oxidation, applicable to both monomers and peptides. By optimizing reagent ratios and pH buffering in Cu(2+) /ascorbate/O2 reaction system, we improved the yield more than tenfold compared to reported conditions, which allowed us to obtain homogeneously modified 2-oxohisidine peptides for further studies. Analysis of 2-oxohistidine-containing model peptides by liquid chromatography-tandem mass spectrometry demonstrated increased retention time in reverse-phase chromatography and general stability of 2-oxohistidine under electrospray ionization and collision-induced dissociation. Thus, large-scale analysis of 2-oxohistidine-modified proteome should be feasible using shotgun protein mass spectrometry, and we were able to observe such peptides in proteomics datasets. The feasibility of acquiring purified peptide probes and peptide antigens containing 2-oxohistidine will help advance the study of this non-enzymatic posttranslational modification.

Oxidative protein labeling with analysis by mass spectrometry for the study of structure, folding, and dynamics

SIGNIFICANCE

Analytical approaches that can provide insights into the mechanistic processes underlying protein folding and dynamics are few since the target analytes-high-energy structural intermediates-are short lived and often difficult to distinguish from coexisting structures. Folding "intermediates" can be populated at equilibrium using weakly denaturing solvents, but it is not clear that these species are identical to those that are transiently populated during folding under "native" conditions. Oxidative labeling with mass spectrometric analysis is a powerful alternative for structural characterization of proteins and transient protein species based on solvent exposure at specific sites.

RECENT ADVANCES

Oxidative labeling is increasingly used with exceedingly short (μs) labeling pulses, both to minimize the occurrence of artifactual structural changes due to the incorporation of label and to detect short-lived species. The recent introduction of facile photolytic approaches for producing reactive oxygen species is an important technological advance that will enable more widespread adoption of the technique.

CRITICAL ISSUES

The most common critique of oxidative labeling data is that even with brief labeling pulses, covalent modification of the protein may cause significant artifactual structural changes.

FUTURE DIRECTIONS

While the oxidative labeling with the analysis by mass spectrometry is mature enough that most basic methodological issues have been addressed, a complete systematic understanding of side chain reactivity in the context of intact proteins is an avenue for future work. Specifically, there remain issues around the impact of primary sequence and side chain interactions on the reactivity of "solvent-exposed" residues. Due to its analytical power, wide range of applications, and relative ease of implementation, oxidative labeling is an increasingly important technique in the bioanalytical toolbox.

Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics

The current advances in mass spectrometry technology have led to the possibility of analyzing more complex biological samples such as entire proteomes. Here, we describe a new and powerful methodology that combines the use of the metalloendopeptidase Lys-N and strong cation exchange with mass spectrometric analysis. The approach described here allows one to separate peptides with different functional groups. The peptides we are able to isolate are N-terminal peptides, phosphorylated peptides with a single lysine, peptides with a single basic residue (lysine), and peptides with multiply basic residues. When this separation strategy is combined with tandem mass spectrometry that involves both collision-induced dissociation and electron transfer dissociation, one can achieve an optimal targeted strategy for proteome analysis.

Role of 2-oxo and 2-thioxo modifications on the proton affinity of histidine and fragmentation reactions of protonated histidine

A combination of electrospray ionisation (ESI), multistage and high-resolution mass spectrometry experiments was used to compare the gas-phase chemistry of the amino acids histidine (1), 2-oxo-histidine (2), and 2-thioxo-histidine (3). Collision-induced dissociation (CID) of all three different proton-bound heterodimers of these amino acids led to the relative gas-phase proton affinity order of: histidine >2-thioxo-histidine >2-oxo-histidine. Density functional theory (DFT) calculations confirm this order, with the lower proton affinities of the oxidised histidine derivatives arising from their ability to adopt the more stable keto/thioketo tautomeric forms. All protonated amino acids predominately fragment via the combined loss of H(2)O and CO to yield a(1) ions. Protonated 2 and 3 also undergo other small molecule losses including NH(3) and the imine HN=CHCO(2)H. The observed differences in the fragmentation pathways are rationalised through DFT calculations, which reveal that while modification of histidine via the introduction of the oxygen atom in 2 or the sulfur atom in 3 does not affect the barriers against the loss of H(2)O+CO, barriers against the losses of NH(3) and HN=CHCO(2)H are lowered relative to protonated histidine.

Oxidative protein labeling in mass-spectrometry-based proteomics

Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)-mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.

Correct identification of oxidized histidine residues using electron-transfer dissociation

Oxidative modification to the side chain of histidine can noticeably change the collision-induced dissociation (CID) pathways of peptides containing this oxidized residue. In cases where an oxidized peptide consists two or more isomers differing only in the site of modification, oxidation to histidine usually causes the other oxidized sites to be mis-assigned in CID spectra. These spectral misassignments can sometimes be avoided by using multiple stages of MS/MS (MS(n)) or via specially optimized liquid chromatographic separation conditions. In this manuscript, we demonstrate that these misassignments can be more readily and easily avoided by using electron-transfer dissociation (ETD) to dissociate the oxidized peptides. Furthermore, we find that the relative insensitivity of ETD to side-chain chemistry allows the extent of oxidative modification to be determined readily for peptide isomers having more than one site of oxidation. The current results along with previous studies of oxidized peptides suggest that ETD is probably a better technique than CID for obtaining correct sequence and modification information for oxidized peptides.

Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation

Oxidative modifications to the side chains of sulfur-containing amino acids often limit the number of product ions formed during collision-induced dissociation (CID) and thus make it difficult to obtain sequence information for oxidized peptides. In this work, we demonstrate that electron-transfer dissociation (ETD) can be used to improve the sequence information obtained from peptides with oxidized cysteine and methionine residues. In contrast to CID, ETD is found to be much less sensitive to the side-chain chemistry, enabling extensive sequence information to be obtained in cases where CID fails to provide this information. These results indicate that ETD is a valuable technique for studying oxidatively modified peptides and proteins. In addition, we report a unique and very abundant product ion that is formed in the CID spectra of peptides having N-terminal cysteine sulfinic acid residues. The mechanism for this unique dissociation pathway involves a six-membered cyclic intermediate and leads to the facile loss of NH(3) and SO(2), which corresponds to a mass loss of 81 Da. While the facile nature of this dissociation pathway limits the sequence information present in CID spectra of peptides with N-terminal cysteine sulfinic acid residues, extensive sequence information for these peptides can be obtained with ETD.