Targeted Bottom–Up Mass Spectrometry Approach for the Relative Quantification of Post-Translational Modification of Bovine κ-Casein during Milk Fermentation

κ-casein (κ-CN) is one of the key components in bovine milk, playing a unique role in the structuration of casein micelles. It contains in its chemical structure up to sixteen amino acid residues (mainly serine and threonine) susceptible to modifications, including glycosylation and phosphorylation, which may further be formed during milk processing. In this study, changes in post-translational modification (PTM) of κ-CN during bovine milk fermentation were investigated. One-to-five-day fermented milk samples were produced. A traditional bottom–up proteomics approach was used to establish a multiple-reaction monitoring (MRM) method for relative quantification of κ-CN PTM. Endoproteinase Glu-C was found to efficiently digest the κ-CN molecule. The developed LC-MS method was validated by performing assessments of linearity, precision, repeatability, reproducibility, limit of detection (LOD), and limit of quantification (LOQ). Among the yielded peptides, four of them containing serine and threonine residues were identified and the unmodified as well as the modified variants of each of them were relatively quantified. These peptides were (1) IPTINTIASGEPTSTTE _{[140, 158]}, (2) STVATLE _{[162, 168]}, (3) DSPE _{[169, 172]}, and (4) INTVQVTSTAV _{[180, 190]}. Distribution analysis between unmodified and modified peptides revealed that over 50% of κ-CN was found in one of its modified forms in milk. The fermentation process further significantly altered the composition between unmodified/modified κ-CN, with glycoslaytion being predominant compared to phosphorylation (p < 0.01). Further method development towards α and β-CN fractions and their PTM behavior would be an asset to better understand the changes undergone by milk proteins and the micellar structure during fermentation.     

Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations

The redox activity of cysteine sulfur allows numerous post‐translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas‐phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSO_x]^? (x=1, 2, 3, representing the number of S‐bound oxygen atoms), which are key intermediates in the redox‐switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur‐containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO^? in [cysSO]^? migrates to the carboxylate in [cysSO₃]^?, whereas it turns out to be shared in [cysSO₂]^?. Evidence is gathered that a mixture of close‐lying low‐energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.     

Label‐Free Quantification of 5‐Azacytidines Directly in the Genome

Azacytidines (AzaC and AzadC) are clinically relevant pharmaceuticals that operate at the epigenetic level. They are integrated into the genome as antimetabolites to block DNA methylation events. This leads to a reduction of the 5‐methyl‐2′‐deoxycytidine (m⁵dC) level in the genome, which can activate epigenetically silenced genes. Because of the inherent chemical instability of Aza(d)Cs, their incorporation levels in DNA and RNA are difficult to determine, which hinders correlation of therapeutic effects with incorporation and removal processes. Existing methods involve radioactive labeling and are therefore unsuitable to monitor levels from patients. We report here a new direct chemical method that allows absolute quantification of the levels of incorporated AzaC and AzadC in both RNA and DNA. Furthermore, it clarifies that Aza(d)C accumulates to high levels (up to 12.9 million bases per genome). Although RNA‐based antimetabolites are often 2′‐deoxygenated in vivo and incorporated into DNA, for AzaC we see only limited incorporation into DNA. It accumulates predominantly in RNA where it, however, only leads to insignificant demethylation.     

Copper‐Catalyzed Aerobic Autoxidation of N‐Hydroxycarbamates Probed by Mass Spectrometry

We present herein a mechanistic investigation by nanoelectrospray ionization mass spectrometry of copper‐catalyzed aerobic oxidative processes involved in the N‐nitrosocarbonyl aldol reaction of N‐hydroxycarbamates. Protonated amine and copper as charge‐tags aided the detection of reaction intermediates, which verified the enamine mechanism together with a competing enol process. Our experimental results reveal that the copper‐catalyzed aerobic oxidation of N‐hydroxycarbamates may proceed through an autoxidation catalytic mechanism in which a CbzNHO^. radical abstracts a hydrogen from the bound N‐hydroxycarbamate to release the nitroso intermediate through a bimolecular hydrogen‐atom transfer. In this process, the chiral diamine also works as a ligand for copper to facilitate the aerobic oxidative step. The dual role of the chiral vicinal diamine as both an aminocatalyst and a bidentate ligand was finally uncovered.     

A Simple Way to Speed up Separations by GC‐MS Using Short 0.53 mm Columns and Vacuum Outlet Conditions

There is a constant drive to speed up GC separations. Shorter analysis times provide more analyses per day, which reduces cost. One approach is to reduce column length and column diameter and columns of 0.15 mm i.d. have indeed grown in popularity. However, the majority of applications are still done with 0.25 mm and 0.32 mm columns.     

Determining sequences and post-translational modifications of novel conotoxins in Conus victoriae using cDNA sequencing and mass spectrometry

A combination of cDNA cloning and detailed mass spectrometric analyses was employed to identify novel conotoxins from Conus victoriae. Eleven conotoxin sequences were determined using molecular methods: one belonging to the A superfamily (Vc1.1), six belonging to the O superfamily (Vc6.1-Vc6.6) and four members of the T superfamily (Vc5.1-Vc5.4). In order to verify the sequences and identify the post-translational modifications (excluding the disulfide connectivity) of three Conus victoriae conotoxins, vc1a, vc5a and vc6a, deduced from sequences Vc1.1, Vc5.1, and Vc6.1, respectively, liquid chromatography/electrospray ionization ion trap mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nanospray ionization ion trap mass spectrometry with collisionally induced dissociation were performed on reduced and alkylated venom fractions. We report that vc1a, the native form of alpha-conotoxin Vc1.1 (an unmodified 16 amino acid residue peptide that has notable pain-relieving capabilities), includes a hydroxyproline and a gamma-carboxyglutamate residue. Conotoxin vc5a is a 10-residue peptide with two disulfide bonds and a hydroxyproline and vc6a is a 25 amino acid peptide with three disulfide bonds.     

Unexpected Acetylation of Endogenous Aliphatic Amines by Arylamine N‐Acetyltransferase NAT2

N‐Acetyltransferases play critical roles in the deactivation and clearance of xenobiotics, including clinical drugs. NAT2 has been classified as an arylamine N‐acetyltransferase that mainly converts aromatic amines, hydroxylamines, and hydrazines. Herein, we demonstrate that the human arylamine N‐acetyltransferase NAT2 also acetylates aliphatic endogenous amines. Metabolomic analysis and chemical synthesis revealed increased intracellular concentrations of mono‐ and diacetylated spermidine in human cell lines expressing the rapid compared to the slow acetylator NAT2 phenotype. The regioselective N⁸‐acetylation of monoacetylated spermidine by NAT2 answers the long‐standing question of the source of diacetylspermidine. We also identified selective acetylation of structurally diverse alkylamine‐containing drugs by NAT2, which may contribute to variations in patient responses. The results demonstrate a previously unknown functionality and potential regulatory role for NAT2, and we suggest that this enzyme should be considered for re‐classification.     

Transformation of the gas‐phase favored O‐protomer of p‐aminobenzoic acid to its unfavored N‐protomer by ion activation in the presence of water vapor: An ion‐mobility mass spectrometry study

An ion‐mobility mass spectrometry study showed that the preferred O‐protonated form of p‐aminobenzoic in the gas phase can be converted to the thermodynamically less favored N‐protomer by in‐source collision‐induced ion activation during the ion transfer process from the atmospheric region to the first vacuum region if the humidity is high in the ion source. Upon the addition of water vapor to the nitrogen gas used to promote the solid analyte to the gas phase under helium‐plasma ionization conditions, the intensity of the ion‐mobility arrival‐time peak for the N‐protomer increased dramatically. Evidently, the ion‐activation process in the first vacuum region is able to provide the energy required to surmount the barrier to isomerize the O‐protomer to the more energetic N‐protomer. The transfer of the proton attached to the carbonyl oxygen atom of the O‐protomer to the amino group takes place by a water‐bridge mechanism. Apparently, the postionization transformations that take place during the transmission of ions from the atmospheric‐pressure ion source to the detector, via different physical compartments of low to high vacuum, play an eminent role in determining the population ratios eventually manifested at the detector.     

Reagent‐free and pH‐independent degradation of N‐nitrosamines using electrons generated via corona discharge at ambient pressure

Traditional degradation methods for N‐nitrosamines are either confined with acid solution or required for additional chemical reagents to guarantee high reaction efficiency. Herein, we demonstrate a facile and effective way for reagent‐free and pH‐independent degradation of N‐nitrosamines, which was induced by free electrons generated via corona discharge at ambient pressure. The highly reactive free electron is produced in situ and responsible for degradation of three N‐nitrosamines, which was also theoretically confirmed. N‐nitrosamines were believed to be reduced by electrons and to form the radical anion, which underwent a selectively heterolytic cleavage of the N–NO bonds to form the corresponding secondary amines as the degradation products.     

A Transformation of N‐Alkylated Anilines to N‐Aryloxamates

Transformation of N‐alkylated anilines to N‐aryloxamates was studied using ethyl 2‐diazoacetoacetate as an alkylating agent and dirhodium tetraacetate (Rh₂(OAc)₄) as the catalyst. The general applicability of the reaction as a synthetic method for N‐aryloxamates was studied with a number of substituted N‐alkylated anilines. The results revealed that the oxamate was formed by a radical reaction with molecular O₂ and Rh₂(OAc)₄ as initiator.     

Quantification of bisphenol A and its selected analogs in serum using pre‐column derivatization with high‐performance liquid chromatography and tandem mass spectrometry

Due to regulation of the use of bisphenol A, several analogs serving as bisphenol A replacements have drawn substantial attention for their adverse health effects. To investigate their occurrence in humans and identify possible pollution sources, it is necessary to develop a sensitive method for total bisphenols detection. Thus, a method based on enzymolysis and liquid‐liquid extraction followed by molecularly imprinted polymer solid‐phase extraction and pre‐column derivatization with high‐performance liquid chromatography and tandem mass spectrometry was proposed. The developed method exhibited superior selectivity and sensitivity. The matrix effect can be eliminated to a great extent. The method detection limits for eight bisphenols were 0.05～0.19 ng/mL. Satisfactory recoveries (71～119%) were obtained by spiking bovine serum at three levels (0.8, 8 and, 20 ng/mL). The method was successfully applied to determine total bisphenols in the serum samples of children. Bisphenol A, bisphenol F, bisphenol S, bisphenol B and bisphenol F were detected with concentrations from below the method detection limit to 1.65, 0.45, 0.79, 2.04 and 0.17 ng/mL, respectively. These results indicate that bisphenol A remains the major pollutant among the studied bisphenols in children, whereas threats from bisphenol A analogs should also be monitored.     

Characterization of N‐Boc/Fmoc/Z‐N′‐formyl‐gem‐diaminoalkyl derivatives using electrospray ionization multi‐stage mass spectrometry

N‐Boc/Fmoc/Z‐N′‐formyl‐gem‐diaminoalkyl derivatives, intermediates particularly useful in the synthesis of partially modified retro‐inverso peptides, have been characterized by both positive and negative ion electrospray ionization (ESI) ion‐trap multi‐stage mass spectrometry (MSⁿ). The MS² collision induced dissociation (CID) spectra of the sodium adduct of the formamides derived from the corresponding N‐Fmoc/Z‐amino acids, dipeptide and tripeptide acids show the [M + Na‐NH₂CHO]⁺ ion, arising from the loss of formamide, as the base peak. Differently, the MS² CID spectra of [M + Na]⁺ ion of all the N‐Boc derivatives yield the abundant [M + Na‐C₄H₈]⁺ and [M + Na‐Boc + H]⁺ ions because of the loss of isobutylene and CO₂ from the Boc protecting function. Useful information on the type of amino acids and their sequence in the N‐protected dipeptidyl and tripeptidyl‐N′‐formamides is provided by MS² and subsequent MSⁿ experiments on the respective precursor ions. The negative ion ESI mass spectra of these oligomers show, in addition to [M‐H]^?, [M + HCOO]^? and [M + Cl]^? ions, the presence of in‐source CID fragment ions deriving from the involvement of the N‐protecting group. Furthermore, MSⁿ spectra of [M + Cl]^? ion of N‐protected dipeptide and tripeptide derivatives show characteristic fragmentations that are useful for determining the nature of the C‐terminal gem‐diamino residue. The present paper represents an initial attempt to study the ESI‐MS behavior of these important intermediates and lays the groundwork for structural‐based studies on more complex partially modified retro‐inverso peptides. Copyright © 2013 John Wiley & Sons, Ltd.     

Fragmentation features of intermolecular cross‐linked peptides using N‐hydroxy‐ succinimide esters by MALDI‐ and ESI‐MS/MS for use in structural proteomics

The use of mass spectrometry coupled with chemical cross‐linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross‐linked peptides. The interpretation of the MS/MS data generated in cross‐linking experiments using N‐hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross‐linked peptides occur when two different peptides are connected by the cross‐linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross‐linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross‐linked peptides present in cross‐linking experiments and be further implemented in search engine's algorithms. Copyright © 2011 John Wiley & Sons, Ltd.