Determination of the Sites of 4-Hydroxy-2-nonenal Adduction to Protein by Electrospray Tandem Mass Spectrometry

Secondary Lipid Oxidation Products as Modulators of Calpain-2 Functionality In Vitro

The objective was to understand the impacts of secondary lipid oxidation products on calpain-2 activity and autolysis and, subsequently, to determine the quantity and localization of modification sites. 2-Hexenal and 4-hydroxynonenal incubation significantly decreased calpain-2 activity and slowed the progression of autolysis, while malondialdehyde had minimal impact on calpain-2 activity and autolysis. Specific modification sites were determined with LC-MS/MS, including distinct malondialdehyde modification sites on the calpain-2 catalytic and regulatory subunits. 2-Hexenal modification sites were observed on the calpain-2 catalytic subunit. Intact protein mass analysis with MALDI-MS revealed that a significant number of modifications on the calpain-2 catalytic and regulatory subunits are likely to exist. These observations confirm that specific lipid oxidation products modify calpain-2 and may affect the calpain-2 functionality. The results of these novel experiments have implications for healthy tissue metabolism, skeletal muscle growth, and post-mortem meat tenderness development.

Post-Translational Chemical Modification of Amyloid-β Peptides by 4-Hydroxy-2-Nonenal

BACKGROUND

The extraction and quantification of amyloid-β (Aβ) peptides in brain tissue commonly uses formic acid (FA) to disaggregate Aβ fibrils. However, it is not clear whether FA can disaggregate post-translationally modified Aβ peptides, or whether it induces artifact by covalent modification during disaggregation. Of particular interest are Aβ peptides that have been covalently modified by 4-hydroxy-2-nonenal (HNE), an oxidative lipid degradation product produced in the vicinity of amyloid plaques that dramatically accelerates the aggregation of Aβ peptides.

OBJECTIVE

Test the ability of FA to disaggregate Aβ peptides modified by HNE and to induce covalent artifacts.

METHODS

Quantitative liquid-chromatography-tandem-mass spectrometry of monomeric Aβ peptides and identify covalently modified forms.

RESULTS

FA disaggregated ordinary Aβ fibrils but also induced the time-dependent formylation of at least 2 residue side chains in Aβ peptides, as well as oxidation of its methionine side chain. FA was unable to disaggregate Aβ peptides that had been covalently modified by HNE.

CONCLUSION

The inability of FA to disaggregate Aβ peptides modified by HNE prevents FA-based approaches from quantifying a pool of HNE-modified Aβ peptides in brain tissue that may have pathological significance.

Approaches to Heterogeneity in Native Mass Spectrometry

Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.

Lipid Peroxidation Products HNE and ONE Promote and Stabilize Alpha-Synuclein Oligomers by Chemical Modifications

The aggregation of α-synuclein (αSN) and increased oxidative stress leading to lipid peroxidation are pathological characteristics of Parkinson's disease (PD). Here, we report that aggregation of αSN in the presence of lipid peroxidation products 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) increases the stability and the yield of αSN oligomers (αSO). Further, we show that ONE is more efficient than HNE at inducing αSO. In addition, we demonstrate that the two αSO differ in both size and shape. ONE-αSO are smaller in size than HNE-αSO, except when they are formed at a high molar excess of aldehyde. In both monomeric and oligomeric αSN, His50 is the main target of HNE modification, and HNE-induced oligomerization is severely retarded in the mutant His50Ala αSN. In contrast, ONE-induced aggregation of His50Ala αSN occurs readily, demonstrating the different pathways for inducing αSN aggregation by HNE and ONE. Our results show different morphologies of the HNE-treated and ONE-treated αSO and different roles of His50 in their modification of αSN, but we also observe structural similarities between these αSO and the non-treated αSO, e.g., flexible C-terminus, a folded core composed of the N-terminal and NAC region. Furthermore, HNE-αSO show a similar deuterium uptake as a previously characterized oligomer formed by non-treated αSO, suggesting that the backbone conformational dynamics of their folded cores resemble one another.

Thermal Instability Induced by 4-Hydroxy-2-Nonenal in Beef Myoglobin

The secondary products of lipid oxidation, such as 4-hydroxy-2-nonenal (HNE), compromise myoglobin (Mb) redox stability and can thus impact thermal stability. Previous studies examined HNE-induced redox instability in beef Mb, whereas investigations are yet to be undertaken to evaluate the relationship between lipid oxidation and thermal stability of beef Mb. Therefore, the objective of the present study was to investigate the direct influence of HNE on thermal stability of beef Mb at meat conditions. Beef oxymyoglobin (0.15 mM) was incubated with HNE (1.0 mM) at pH 5.6 and 4°C for 21 d in the dark. Metmyoglobin formation, percentage Mb denaturation (PMD), and HNE adduction sites in Mb were examined on days 0, 7, 14, and 21. The experiment was replicated 3 times (n = 3). The data were evaluated using the MIXED procedure of SAS, and the differences among means were detected at the 5% level using the least significant difference test. The HNE-treated samples exhibited greater (P < 0.05) metmyoglobin formation and PMD than the controls. Additionally, the PMD difference between HNE-treated and control samples increased (P < 0.05) over time. Mass spectrometric analyses indicated that the number of HNE adduction sites increased with storage, and 6 histidines (positions 24, 36, 64, 93, 113, and 152) were adducted on day 21. HNE adduction at the distal histidine (position 64), which is critical to he me stability, was observed only on days 14 and 21. An increase in PMD on days 14 and 21 in HNE-treated samples could be partially due to the adduction at distal histidine. These findings indicated that HNE compromises thermal stability of beef Mb, possibly through altering the conformation of the heme protein by nucleophilic adduction.

Carbon Chain Length of Lipid Oxidation Products Influence Lactate Dehydrogenase and NADH-Dependent Metmyoglobin Reductase Activity

The biochemical basis of lower metmyoglobin reducing activity (MRA) in high-oxygen modified atmospheric packaged (HiOx-MAP) beef than those in vacuum and polyvinyl chloride (PVC) packaging is not clear. To explore this, the effects of lipid oxidation products with varying carbon chain length on lactate dehydrogenase (LDH) and NADH-dependent metmyoglobin reductase activity were evaluated. Surface color, MRA, and lipid oxidation of beef longissimus lumborum steaks (n = 10) were measured during 6-day display. Further, two enzymes, LDH and NADH-dependent metmyoglobin reductase (n = 5), critical for MRA were incubated with or without (control) lipid oxidation products of varying carbon chain length: malondialdehyde (3-carbon), hexenal (6-carbon), and 4-hydroxynonenal (9-carbon). Steaks in HiOx-MAP had greater (P < 0.05) redness than vacuum and PVC, but had lower (P < 0.05) MRA and greater (P < 0.05) lipid oxidation on day 6. LDH and NADH-dependent metmyoglobin reductase activities were differentially influenced by lipid oxidation products (P < 0.05). The results indicate that the difference in reactivity of various lipid oxidation products on LDH (HNE > MDA = hexenal) and NADH-dependent metmyoglobin reductase (HNE = MDA > hexenal) activity could be responsible for lower MRA in HiOx-MAP.

Porcine oxymyoglobin and lipid oxidation in vitro

The present study was carried out to investigate the effect of dietary α-tocopherol supplementation on porcine oxymyoglobin (OxyMb) and lipid oxidation (TBARS) in model lipid systems, and to determine the influence of 4-hydroxynonenal (4-HNE), a secondary product of lipid oxidation, on porcine OxyMb stability. Porcine metmyoglobin (MetMb) formation was greater in the presence of 4-HNE than the control (P<0.05). Western blot analyses confirmed the covalent modification of myoglobin (Mb) histidine residues by 4-HNE. When combined with microsomes, both equine and porcine OxyMb oxidation increased with time of incubation, and was greater at 37 than at 25 °C (P<0.05). Lower TBARS values were observed in microsomes prepared from vitamin E-supplemented than control pork livers (P<0.05). α-Tocopherol concentration did not affect OxyMb oxidation in microsomes at 25 or 37 °C (P>0.05). These results differ from those observed with beef muscle microsomes where both OxyMb and lipid oxidation were delayed with elevated α-tocopherol levels. These results suggest that the factors affecting Mb and lipid oxidation interactions may be species-dependent.

Carbonylation of mitochondrial aconitase with 4-hydroxy-2-(E)-nonenal: localization and relative reactivity of addition sites

Mass spectrometry was used to investigate the effects of exposing mitochondrial aconitase (ACO2) to the membrane lipid peroxidation product, 4-hydroxy-2-(E)-nonenal (HNE). ACO2 was selected for this study because (1) it is known to be inactivated by HNE, (2) elevated concentrations of HNE-adducted ACO2 have been associated with disease states, (3) extensive structural information is available, and (4) the iron-sulfur cluster in ACO2 offers a critical target for HNE adduction. The aim of this study was to relate the inactivation of ACO2 by HNE to structural features. Initially, Western blotting and an enzyme activity assay were used to assess aggregate effects and then gel electrophoresis, in-gel digestion, and tandem mass spectrometry (MS/MS) were used to identify HNE addition sites. HNE addition reaction rates were determined for the most significant sites using the iTRAQ approach. The most reactive sites were Cys(358), Cys(421), and Cys(424), the three iron-sulfur cluster-coordinating cysteines, Cys(99), the closest non-ligated cysteine to the cluster, and Cys(565), which is located in the cleft leading to the active site. Interestingly, both enzyme activity assay and iTRAQ relative abundance plots appeared to be trending toward horizontal asymptotes, rather than completion.

In vitro interactions of biological nucleophiles with fluorotelomer unsaturated acids and aldehydes: fate and consequences

Fluorotelomer unsaturated aldehydes and acids (FTUALs and FTUCAs) are intermediate metabolites that form from the biotransformation of fluorotelomer-based chemicals. FTUALs and FTUCAs have been previously suggested to contribute to the toxicity associated with human exposure to fluorotelomer compounds by covalently binding to biological nucleophiles. However, the extent of their reactivity has only been assessed with glutathione. The purpose of the present study was to assess the reactivity of these intermediate metabolites with a series of nucleophilic amino acids and model proteins. In vitro experiments were carried out in an aqueous buffer system to determine the reactivity of nucleophilic amino acids with FTUCAs and FTUALs having varying fluorinated chain lengths. Using (19)F NMR spectroscopy to monitor the disappearance of the FTUCAs and FTUAL signals and the production of a fluoride signal, reaction rate constants were determined under pseudo-first-order conditions. The FTUCAs reacted only with cysteine with the following second order rate constants: 3.63 (± 1.37) × 10(-5) min(-1) mM(-1) (4:2 FTUCA), 1.19 (± 0.91) × 10(-5) min(-1) mM(-1) (6:2 FTUCA), and 4.56 (± 0.94) × 10(-5) min(-1) mM(-1) (8:2 FTUCA). The FTUALs were significantly more reactive than any of the FTUCAs with reactivity decreasing in the following order: cysteine >> histidine > lysine >> arginine. The following second-order rate constants were obtained: 5.7 (± 4.2) × 10(-4) min(-1) mM(-1) (histidine), 4.3 (± 1.4) × 10(-4) min(-1) mM(-1) (lysine), and 1.4 (± 0.73) × 10(-4) min(-1) mM(-1) (arginine). FTUCAs and FTUALs were also reacted with model proteins to assess their potential for forming covalent adducts. Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the stoichiometry of FTUCAs and FTUALs covalently bound to apomyoglobin (ApoMg) and human serum albumin (HSA). FTUCAs were not reactive, whereas two measurable FTUAL adducts were formed with both ApoMg and HSA at each of the FTUAL chain lengths (6:2, 8:2, and 10:2). This is the first study to probe the reactivity of FTUALs and FTUCAs with nucleophiles other than glutathione, further elucidating possible FTUAL and FTUCA fate within biological systems.

The reactivity of human serum albumin toward trans-4-hydroxy-2-nonenal

Mass spectrometry was used to probe the preferred locations of trans-4-hydroxy-2-nonenal (HNE) addition to the cysteine, histidine, and lysine residues of human serum albumin (HSA). Considering only those modified peptides supported by high mass accuracy Orbitrap precursor ion measurements (high confidence hits), with HNE:HSA ratios of 1:1 and 10:1, 3 and 15 addition sites, respectively, were identified. Using less stringent criteria, a total of 34 modifications were identified at the higher concentration. To gain quantitative data, iTRAQ labeling studies were completed. Previous work had identified Cys(34) , the only free cysteine, as the most reactive residue in HSA, and we have found that Lys(199) , His(242/7) , and His(288) are the next most reactive residues. Although the kinetic data indicate that the lysines and histidines can react at relatively similar rates, the results show that lysine addition is much less favorable thermodynamically; under our reaction conditions, lysine addition generally does not go to completion. This suggests that under physiological conditions, HNE addition to lysine is only relevant in situations where unusually high HNE concentrations or access to irreversible secondary reactions are found.

Application of medical and analytical methods in Lyme borreliosis monitoring

Lyme borreliosis (LB) is one of the most common tick-borne diseases in the northern hemisphere. It is a chronic inflammatory disease caused by the spirochaete Borrelia burgdorferi. In its early stages, pathological skin lesions, namely erythema chronicum migrans, appear. The lesions, usually localised at the site of the bite, may become visible from a few weeks up to 3 months after the infection. Predominant clinical symptoms of the disease also involve joint malfunctions and neurological or cardiac disorders. Lyme disease, in all its stages, may be successfully treated with antibiotics. The best results, however, are obtained in its early stages. In order to diagnose the disease, numerous medical or laboratory techniques have been developed. They are applied to confirm the presence of intact spirochaetes or spirochaete components such as DNA or proteins in tick vectors, reservoir hosts or patients. The methods used for the determination of LB biomarkers have also been reviewed. These biomarkers are formed during the lipid peroxidation process. The formation of peroxidation products generated by human organisms is directly associated with oxidative stress. Apart from aldehydes (malondialdehyde and 4-hydroxy-2-nonenal), many other unsaturated components such as isoprostenes and neuroprostane are obtained. The fast determination of these compounds in encephalic fluid, urine or plasma, especially in early stages of the disease, enables its treatment. Various analytical techniques which allow the determination of the aforementioned biomarkers have been reported. These include spectrophotometry as well as liquid and gas chromatography. The analytical procedure also requires the application of a derivatization step by the use of selected reagents.

A mass spectrometric analysis of 4-hydroxy-2-(E)-nonenal modification of cytochrome c

Cytochrome c is a key mitochondrial respiratory protein that is particularly susceptible to modification during oxidative stress. The nature of this susceptibility is linked to the mitochondrial membrane being rich in esterified linoleic acid, which predisposes this organelle to the formation of lipid peroxidation products such as 4-hydroxy-2-(E)-nonenal (4-HNE). To better understand the nature of cytochrome c modification by 4-HNE, we initiated an in vitro study utilizing a combination of MALDI-TOF mass spectrometry, LC-ESI-MS/MS and isotope labeling to monitor 4-HNE modification of cytochrome c under various conditions. The overwhelming reaction observed is Michael addition by Lys side-chains in addition to the modification of His 33. While the Lys-4-HNE adducts were generally observed to be reversible, the 4-HNE-His 33 was observed to be stable with half of the formed adduct surviving the denaturation and proteolysis protocols used to generate proteolytic peptides for LC-ESI-MS/MS.

Analysis of interactions of brevetoxin-B and human serum albumin by liquid chromatography/mass spectrometry

Brevetoxins are neurotoxins produced by marine dinoflagellates, primarily Karenia brevis, and can cause intoxication and even mortality of marine species, affect human health through the consumption of brevetoxin-contaminated shellfish, and effect respiratory irritation through aerosol exposure at coastal areas. Brevetoxin-A and brevetoxin-B, the major brevetoxins produced in algae, are metabolized to a series of amino acid and peptide-related derivatives in shellfish through the reactions of the amino acid residue cysteine with an α,β-unsaturated aldehyde group. In this paper, covalent interactions between brevetoxin and proteins were investigated using brevetoxin-B and human serum albumin (HSA) as a model. It is demonstrated that both noncovalent and covalent interactions can occur between brevetoxin-B and HSA with in vitro experiments. Covalent adducts of brevetoxin-B and HSA were generated under physiological conditions and reduced with sodium borohydride based on the reaction conditions of single amino acid residues with brevetoxin-B. LC/MS analysis of toxin-treated HSA recognized the formation of the intact protein adducts with primarily one and two toxin molecules attached to one HSA molecule. HSA treated with/without brevetoxin-B was digested with trypsin, trypsin following chymotrypsin, and Pronase, respectively, for LC/MS analysis of adduction sites. Brevetoxin-B was found to react primarily with Cys(34) and His(3) and with His and Lys at other sites of HSA with variable reactivity and with Lys in general the least reactive.

Proteomic identification of carbonylated proteins and their oxidation sites

Excessive oxidative stress leaves a protein carbonylation fingerprint in biological systems. Carbonylation is an irreversible post-translational modification (PTM) that often leads to the loss of protein function and can be a component of multiple diseases. Protein carbonyl groups can be generated directly (by amino acids oxidation and the alpha-amidation pathway) or indirectly by forming adducts with lipid peroxidation products or glycation and advanced glycation end-products. Studies of oxidative stress are complicated by the low concentration of oxidation products and a wide array of routes by which proteins are carbonylated. The development of new selection and enrichment techniques coupled with advances in mass spectrometry are allowing the identification of hundreds of new carbonylated protein products from a broad range of proteins located at many sites in biological systems. The focus of this review is on the use of proteomics tools and methods to identify oxidized proteins along with specific sites of oxidative damage and the consequences of protein oxidation.

Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry

Proteomic characterization of carbonylated amino acid sites currently relies on confidently matching tandem mass spectra (MS(2)) to peptides within a sequence database. Although effective to some degree, reliable proteomic characterization of carbonylated peptides using this approach remains a challenge needing new, complementary solutions. To this end, we developed a method based on partial (18)O-labeling of reactive carbonyl modifications, which produces a unique isotope signature in mass spectra of carbonylated peptides and enables their detection without reliance on matching MS(2) spectra to a peptide sequence. Key to our method were optimized measures for eliminating trypsin-catalyzed incorporation of (18)O at peptide C-termini, and for stabilizing the incorporated (18)O within the carbonyl modification to prevent its loss during liquid chromatography separation. Applying our method to a rat skeletal muscle homogenate treated with the carbonyl modification 4-hyroxynonenal (4-HNE), we demonstrated its compatibility with solid-phase hydrazide enrichment of carbonylated peptides from complex mixtures. Additionally, we demonstrated the value of (18)O isotope signatures for confirming HNE-modified peptide sequences matched via sequence database searching, and identifying modified peptides missed by MS(2) and/or sequence database searching. Combining our (18)O-labeling method with a customized automated software script, we systematically evaluated for the first time the efficiency of MS(2) and sequence database searching for identifying HNE-modified peptides. We estimated that less than half of the modified peptides selected for MS(2) were successfully identified. Collectively, our method and software should provide valuable new tools for investigators studying protein carbonylation via mass spectrometry-based proteomics.

Mapping oxidations of apolipoprotein B-100 in human low-density lipoprotein by liquid chromatography-tandem mass spectrometry

Human low-density lipoprotein (LDL) is a major cholesterol carrier in blood. Elevated concentration of low-density lipoprotein, especially when oxidized, is a risk factor for atherosclerosis and other cardiac inflammatory diseases. Past research has connected free radical initiated oxidations of LDL with the formation of atherosclerotic lesions and plaque in the arterial wall. The role of LDL protein in the associated diseases is still poorly understood, partially due to a lack of structural information. In this study, LDL was oxidized by hydroxyl radical. The oxidized protein was then delipidated and subjected to trypsin digestion. Peptides derived from trypsin digestion were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Identification of modified peptide sequences was achieved by a database search against apo B-100 protein sequences using the SEQUEST algorithm. At different hydroxyl radical concentrations, oxidation products of tyrosine, tryptophan, phenylalanine, proline, and lysine were identified. Oxidized amino acid residues are likely located on the exterior of the LDL particle in contact with the aqueous environment or directly bound to the free radical permeable lipid layer. These modifications provided insight for understanding the native conformation of apo B-100 in LDL particles. The presence of some natural variants at the protein level was also confirmed in our study.

Identification of carbonylation sites in apomyoglobin after exposure to 4-hydroxy-2-nonenal by solid-phase enrichment and liquid chromatography-electrospray ionization tandem mass spectrometry

Identification of protein carbonylation because of covalent attachment of a lipid peroxidation end-product was performed by combining proteolytic digestion followed by solid-phase hydrazide enrichment and liquid chromatography (LC)-electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using both collision-induced dissociation (CID) and electron capture dissociation (ECD). To evaluate this approach, we selected apomyoglobin and 4-hydroxy-2-nonenal (4-HNE) as a model protein and a representative end-product of lipid peroxidation, respectively. Although the characteristic elimination of 4-HNE (156 Da) in CID was found to serve as a signature tag for the modified peptides, generation of nearly complete fragment ion series because of efficient peptide backbone cleavage (in most cases over 75%) and the capability to retain the labile 4-HNE moiety of the tryptic peptides significantly aided the elucidation of primary structural information and assignment of exact carbonylation sites in the protein, when ECD was employed. We have concluded that solid-phase enrichment with both CID- and ECD-MS/MS are advantageous during an in-depth interrogation and unequivocal localization of 4-HNE-induced carbonylation of apomyoglobin that occurs via Michael addition to its histidine residues.

Biodiesel production from sunflower, soybean, and waste cooking oils by transesterification using lipase immobilized onto a novel microporous polymer

This study aims at carrying out lipase-catalyzed synthesis of fatty acid methyl esters (biodiesel) from various vegetable oils using lipase immobilized onto a novel microporous polymeric matrix (MPPM) as a low-cost biocatalyst. The research is focused on three aspects of the process: (a) MPPM synthesis (monolithic, bead, and powder forms), (b) microporous polymeric biocatalyst (MPPB) preparation by immobilization of lipase onto MPPM, and (c) biodiesel production by MPPB. Experimental planning of each step of the study was separately carried out in accordance with design of experiment (DoE) based on Taguchi methodology. Microporous polymeric matrix (MPPM) containing aldehyde functional group was synthesized by polyHIPE technique using styrene, divinylbenzene, and polyglutaraldehyde. Thermomyces lanuginosus lipase was covalently attached onto MPPM with 80%, 85%, and 89% immobilization efficiencies using bead, powder, and monolithic forms, respectively. Immobilized enzymes were successfully used for the production of biodiesel using sunflower, soybean, and waste cooking oils. It was shown that immobilized enzymes retain their activities during 10 repeated batch reactions at 25 degrees C, each lasting 24h. Since the developed novel method is simple yet effective, it could have a potential to be used industrially for the production of chemicals requiring immobilized lipases.

Development of a derivatisation method for the analysis of aldehyde modified amino acid residues in proteins by Fourier transform mass spectrometry

A method was developed for the analysis of amino acids within bovine serum albumin (BSA) which had been modified by reaction with different enals. BSA was reacted with the aldehydes and the reaction products were stabilised by reaction with NaBH(4). The protein was then hydrolysed with 6N HCl and the hydrolysis products were analysed by liquid chromatography-mass spectrometry (LC-MS). The modified amino acids were derivatised with propylchloroformate. High resolution mass spectrometry carried out using an LTQ-Orbitrap instrument which was able to characterise a wide range of adducts. In addition double adducts were observed to be formed with 4-hydroxynonenal (HNE) and lysine or lysine+histidine. Qualitatively it was possible to consistently observe a pyridinium adduct formed between lysine and pentenal in human plasma from normal subjects.

Rapid characterization of covalent modifications to rat brain mitochondrial proteins after ex vivo exposure to 4-hydroxy-2-nonenal by liquid chromatography-tandem mass spectrometry using data-dependent and neutral loss-driven MS3 acquisition

The modification of mitochondrial proteins enriched from rat forebrain by the major lipid peroxidation product 4-hydroxy-2-nonenal (HNE) was investigated using high performance liquid chromatography (HPLC) and tandem mass spectrometry. Subcellular fractionation in conjunction with a 'shotgun-based' approach that involved both conventional data-dependent and neutral loss (NL)-driven MS(3) data acquisition on a hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (LTQ-FT) was utilized. Using a relatively rapid linear HPLC gradient (1 h) for complex mixture analysis, 24 sites of HNE modification on 15 unique proteins were identified which corresponded exclusively to Michael adduct formation on histidine residues. Since a number of HNE-modified peptides produced a predominant HNE NL fragment-ion signal upon collision-induced dissociation (CID), NL-driven MS(3) data-dependent acquisition was a valuable method to enhance fragmentation information for these particular modified peptides. Of the 24 HNE modification sites identified, approximately 25% were determined from the MS(3) spectra alone. We envision the reported methodology as an efficient screening approach for HNE modification site selectivity that could ultimately provide a foundation for the development of targeted schemes for the characterization of in vivo HNE-protein adducts.

HNE Michael adducts to histidine and histidine-containing peptides as biomarkers of lipid-derived carbonyl stress in urines: LC-MS/MS profiling in Zucker obese rats

A new liquid chromatography-tandem mass spectrometric (LC-MS/MS) approach, based on the precursor ion scanning technique using a triple-stage quadrupole, has been developed to detect free and protein-bound histidine (His) residues modified by reactive carbonyl species (RCS) generated by lipid peroxidation. This approach has been applied to urines from Zucker obese rats, a nondiabetic animal model characterized by obesity and hyperlipidemia, where RCS formation plays a key role in the development of renal and cardiac dysfunction. The immonium ion of His at m/z 110 was used as a specific product ion of His-containing peptides to generate precursor ion spectra, followed by MS2 acquisitions of each precursor ion of interest for structural characterization. By this approach, three novel adducts, which are excreted in free form only, have been identified, two of them originating from the conjugation of 4-hydroxy-trans-2-nonenal (HNE) to His, followed by reduction/oxidation of the aldehyde: His-1,4-dihydroxynonane (His-DHN), His-4-hydroxynonanoic acid (His-HNA), and carnosine-HNE, this last recognized in previous in vitro studies as a new potential biomarker of carbonyl stress. No free His-HNE was found in urines, which was detected only in protein hydrolysates. The same LC-MS/MS method, working in multiple reaction monitoring (MRM) mode, has been developed, validated, and applied to quantitatively profile in Zucker urines both conventional (1,4-dihydroxynonane mercapturic acid, DHN-MA) and the newly identified adducts, except His-HNA. The analytes were separated on a C12 reversed-phase column by gradient elution from 100% A (water containing 5 mM nonafluoropentanoic acid) to 80% B (acetonitrile) in 24 min at a flow rate of 0.2 mL/min and analyzed for quantification in MRM mode by applying the following precursor-to-product ion transitions m/z 322.2 --> 164.1 + 130.1 (DHN-MA), m/z 314.7 --> 268.2 + 110.1 (His-DHN), m/z 312.2 --> 110.1 + 156.0 (His-HNE), m/z 383.1 --> 266.2 + 110.1 (CAR-HNE), m/z 319.2 --> 301.6 + 156.5 (H-Tyr-His-OH, internal standard). Precision and accuracy data, as well as the lower limits of quantification in urine, were highly satisfactory (from 0.01 nmol/mL for CAR-HNE, His-DHN, His-HNE, to 0.075 nmol/mL for DHN-MA). The method, applied to evaluate for the first time the advanced lipoxidation end products profile in urine from obese Zucker rats, an animal model for the metabolic syndrome, has proved to be suitable and sensitive enough for testing in vivo the carbonyl quenching ability of newly developed RCS sequestering agents.

Enhancement of the stability of a prolipase from Rhizopus oryzae toward aldehydes by saturation mutagenesis

A prolipase from Rhizopus oryzae (proROL) was engineered in order to increase its stability toward lipid oxidation products such as aldehydes with the aim of improving its performance in oleochemical industries. Out of 22 amino acid residues (15 Lys and 7 His) prone to react with aldehydes, 6 Lys and all His residues (except for the catalytic histidine) were chosen and subjected to saturation mutagenesis. In order to quickly and reliably identify stability mutants within the resulting libraries, active variants were prescreened by an activity staining method on agar plates. Active mutants were expressed in Escherichia coli Origami in a 96-well microtiterplate format, and a stability test using octanal as a model deactivating agent was performed. The most stable histidine mutant (H201S) conferred a stability increase of 60%, which was further enhanced to 100% by combination with a lysine mutant (H201S/K168I). This increase in stability was also confirmed for other aldehydes. Interestingly, the mutations did not affect specific activity, as this was still similar to the wild-type enzyme.

Fourier transform ion cyclotron resonance mass spectrometry of covalent adducts of proteins and 4-hydroxy-2-nonenal, a reactive end-product of lipid peroxidation

Covalent adduction of the model protein apomyoglobin by 4-hydroxy-2-nonenal, a reactive end-product of lipid peroxidation, was characterized by nanoelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The high mass resolving power and mass measurement accuracy of the instrument facilitated a detailed compositional analysis of the complex reaction product without the need for deconvolution and transformation to clearly show the pattern of adduction and component molecular weights. Our study has also demonstrated the value of electron capture dissociation over collision-induced dissociation for the tandem mass spectrometric determination of site modification for the 4-hydroxy-2-nonenal adduct of oxidized insulin B chain as an example.

Analysis of modified apolipoprotein B-100 structures formed in oxidized low-density lipoprotein using LC-MS/MS

Oxidatively modified low-density lipoprotein (oxLDL) is one of the major factors involved in the development of atherosclerosis. Because of the insolubility of apolipoprotein B-100 (apoB-100) and the heterogeneous nature of oxidative modification, modified structures of apoB-100 in oxLDL are poorly understood. We applied an on-Membrane sample preparation procedure for LC-MS/MS analysis of apoB-100 proteins in native and modified low-density lipoprotein (LDL) samples to eliminate lipid components in the LDLs followed by collection of tryptic digests of apoB-100. Compared with a commonly used in-gel digestion protocol, the sample preparation procedure using PVDF membrane greatly increased the recovery of tryptic peptides and resulted in improved sequence coverage in the final analysis, which lead to the identification of modified amino acid residues in copper-induced oxLDL. A histidine residue modified by 4-hydroxynonenal, a major lipid peroxidation product, as well as oxidized histidine and tryptophan residues were detected. LC-MS/MS in combination with the on-Membrane sample preparation procedure is a useful method to analyze highly hydrophobic proteins such as apoB-100.

active site modifications of the brain isoform of creatine kinase by 4-hydroxy-2-nonenal correlate with reduced enzyme activity: mapping of modified sites by Fourier transform-ion cyclotron resonance mass spectrometry

Creatine kinase reversibly catalyzes the transfer of the high-energy phosphoryl group from phosphocreatine to MgADP for rapid regeneration of ATP. It is hypothesized that factors which perturb creatine kinase activity, such as reactive oxygen species resulting from oxidative stress, could have a major role in the pathogenesis of diseases, particularly in the brain, where the level of ATP utilization is high. The reactive aldehyde 4-hydroxy-2-nonenal is a major secondary product of lipid peroxidation caused by oxidative stress; the levels of both free and protein-bound 4-hydroxy-2-nonenal are increased in Alzheimer's disease brain. Preliminary reports indicated that creatine kinase had lower activity in Alzheimer's disease brain. In this study, we investigated the structural and functional consequences of reacting the cytosolic brain isoform of creatine kinase with 4-hydroxy-2-nonenal at pathophysiologically relevant concentrations of 4-hydroxy-2-nonenal (10-300 microM). Dose-dependent reduction of enzyme activity was observed and, for the first time, correlated with 4-hydroxy-2-nonenal adduct formation on specific amino acid residues, including the active site residues His66, His191, Cys283, and His296 as determined by Fourier transform-ion cyclotron resonance mass spectrometry.

Collision-induced reporter fragmentations for identification of covalently modified peptides

Collision-induced reporter fragmentations of the currently most important covalent peptide modifications as detected by tandem mass spectrometry are summarized. These fragmentations comprise the formation of reporter ions, which are preferentially immonium ions, immonium ion-derived fragments or side chain fragments. In addition, the reporter neutral loss reactions for covalently modified amino acid residues are summarized. For each individual covalent modification which can be recognized by a reporter fragmentation, the accurate mass shift and the gross formula shift of the modified amino acid residue are given. The same set of data is provided for the reporter fragmentations. Finally, an extensive accurate mass and gross formula list is presented as supplementary material, describing mostly regular and modified y(1) and dipeptide a and b ions, which are helpful for identification of the peptide ends of covalently modified peptides.

Covalent modification of cytochrome c exposed to trans,trans-2,4-decadienal

Modification of biomolecules by reactive aldehydes is believed to play a role in biological processes, including aging, atherosclerosis, and Alzheimer's disease. Here, the modification of cytochrome c promoted by trans, trans-2,4-decadienal (DDE) was investigated. Matrix-assisted laser desorption/ionization time-of-flight experiments indicated increases in the molecular weight of cytochrome c, consistent with the formation of DDE adducts. Our data show that the protein modification was time-, pH-, and DDE concentration-dependent, leading to the formation of at least six adducts after 2 h of incubation at pH 7.4. Electrospray ionization quantitative TOF mass spectrometry analysis of tryptic digests indicated that His-33, Lys-39, Lys-72, and Lys-100 were modified by DDE. These adducts could have significant effects considering that His-33, Lys-72, and Lys-100 are present in clusters of basic amino acid residues, which are believed to participate in the interaction of cytochrome c with cardiolipin in the inner mitochondrial membrane and cytochrome c oxidase. A blue shift in the cytochrome c Soret band from 409 to 406 nm was also observed after DDE reaction, indicating heme crevice opening and displacement of heme sixth ligand (Met-80) coordination in modified protein. The covalent modifications in cytochrome c could play a role in mitochondrial dysfunction associated with oxidative stress.

Proteomic Mapping of 4-Hydroxynonenal Protein Modification Sites by Solid-Phase Hydrazide Chemistry and Mass Spectrometry

The modification of proteins by the cytotoxic, reactive aldehyde 4-hydroxynonenal (HNE) is known to alter protein function and impair cellular mechanisms. In order to identify susceptible amino acid sites of HNE modification within complex biological mixtures by microcapillary liquid chromatography and linear ion trap tandem mass spectrometry, we have developed a solid-phase capture and release strategy that utilizes reversible hydrazide chemistry to enrich HNE-modified peptides. To maximize the detection of fragment ions diagnostic of HNE modification, both neutral loss-dependent acquisition of MS/MS/MS spectra and the pulsed Q dissociation operation mode were employed. When the solid-phase hydrazide enrichment strategy was applied to a yeast lysate treated with HNE, 125 distinct amino acid sites of HNE modification were mapped on 67 different proteins. The endogenous susceptibility of many of these proteins to HNE modification was demonstrated by analyzing HNE-treated yeast cell cultures with a complementary biotin hydrazide enrichment strategy. Further analysis revealed that the majority of amino acid sites susceptible to HNE modification were histidine residues, with most of these sites being flanked by basic amino acid residues, and predicted to be solvent exposed. These results demonstrate the effectiveness of this novel strategy as a general platform for proteome-scale identification of amino acid sites susceptible to HNE modification from within complex mixtures.

Proteomics of lipid oxidation-induced oxidation of porcine and bovine oxymyoglobins

Myoglobin (Mb) redox state affects meat color and is destabilized by lipid oxidation products such as 4-hydroxy-2-nonenal (HNE). Our objective was to investigate lipid oxidation-induced oxymyoglobin (OxyMb) oxidation in Mb from two major meat-producing livestock species utilizing MS and proteomics tools. Porcine OxyMb was incubated with HNE and analyzed for metmyoglobin (MetMb) formation. MetMb formation was greater in the presence of HNE than controls at pH 7.4 and 37 degrees C (p <0.05). MALDI-TOF MS was used to identify adduct formation; only mono-adducts of HNE (via Michael addition) with porcine Mb were detected. LC-ESI-MS/MS identified three histidine (HIS) residues in porcine Mb that were readily adducted by HNE (HIS 24, 36 and 119), whereas in bovine Mb seven histidine residues (HIS 24, 36, 81, 88, 93, 119 and 152) were adducted. Quantitation of HNE-adducted peptides using isotope-labeled phenyl isocyanate indicated that, initially, HIS 36 was preferentially adducted in porcine Mb whereas HIS 81, 88 and 93 were the predominant sites of early HNE adduction in bovine Mb. Preferential HNE adduction at the proximal histidine (HIS 93) was observed exclusively in bovine OxyMb and may explain why lipid oxidation-induced OxyMb oxidation appears more extensive in beef, than in pork.

Membrane-mediated amyloidogenesis and the promotion of oxidative lipid damage by amyloid beta proteins

Evidence of oxidative stress and the accumulation of fibrillar amyloid beta proteins (Abeta) in senile plaques throughout the cerebral cortex are consistent features in the pathology of Alzheimer disease. To define a mechanistic link between these two processes, various aspects of the relationship between oxidative lipid membrane damage and amyloidogenesis were characterized by chemical and physical techniques. Earlier studies of this relationship demonstrated that oxidatively damaged synthetic lipid membranes promoted amyloidogenesis. The studies reported herein specify that 4-hydroxy-2-nonenal (HNE) is produced in both synthetic lipids and human brain lipid extracts by oxidative lipid damage and that it can account for accelerated amyloidogenesis. Abeta promotes the copper-mediated generation of HNE from polyunsaturated lipids, and in turn, HNE covalently modifies the histidine side chains of Abeta. HNE-modified Abeta have an increased affinity for lipid membranes and an increased tendency to aggregate into amyloid fibrils. Thus, the prooxidant activity of Abeta leads to its own covalent modification and to accelerated amyloidogenesis. These results illustrate how lipid membranes may be involved in templating the pathological misfolding of Abeta, and they suggest a possible chemical mechanism linking oxidative stress with amyloid formation.

Redox instability induced by 4-hydroxy-2-nonenal in porcine and bovine myoglobins at pH 5.6 and 4 degrees C

Myoglobin (Mb) redox stability affects meat color and is compromised by lipid oxidation products such as 4-hydroxy-2-nonenal (HNE). Pork lipids are generally more unsaturated and would be expected to oxidize readily and produce more oxidation products than beef. Supranutritional supplementation of vitamin E improves Mb redox stability of beef but not pork. The present study investigated HNE-induced redox instability in porcine and bovine myoglobins at 4 degrees C and pH 5.6. Oxymyoglobin (OxyMb) was incubated with HNE (0.075 mM porcine OxyMb + 0.5 mM HNE; 0.15 mM bovine OxyMb + 1.0 mM HNE). In porcine Mb, only monoadducts formed via Michael addition were detected after 72 h, whereas in bovine Mb both mono- and diadducts were identified. LC-MS-MS identified four histidine residues (His 36, 81, 88, and 152) of bovine Mb that were readily adducted by HNE, whereas in porcine Mb only two histidine residues (His 24 and 36) were adducted. These results suggested that the primary structure of bovine Mb predisposes it to greater nucleophilic attack by HNE and subsequent adduction than is suffered by porcine Mb.

Contribution of mass spectrometry to assess quality of milk-based products

The vast knowledge of milk chemistry has been extensively used by the dairy manufacturing industry to develop and optimize the modern technology required to produce high-quality milk products to which we are accustomed. A thorough understanding of the chemistry of milk and its numerous components is essential for designing processing equipment and conditions needed for the manufacture and distribution of high-quality dairy products. Knowledge and application of milk chemistry is also indispensable for fractionating milk into its principal components for use as functional and nutritional ingredients by the food industry. For all these reasons, powerful analytical methods are required. Because of the complexity of the milk matrix, mass spectrometry, coupled or not to separation techniques, constitutes a key tool in this area. In the present manuscript, we review the contribution and potentialities of mass spectrometry-based techniques to assess quality of milk-based products.

Method for determining the average degree of substitution of o-vanillin derivatized porcine somatotropin

Electrospray mass spectral observation directly on a sample of a derivatized protein, such as porcine somatotropin (pST), affords a method for evaluating the degree of substitution of this protein. Derivatization of the lysine residues and the terminal amino residue here by formation of a Schiff base with a small aromatic aldehyde (in this case, o-vanillin) affords stabilization of the protein so that it may be used in a controlled release veterinary pharmaceutical formulation. This method permits direct observation of substitutions, optimization of manufacturing procedures for producing a commercial product, and permits quality evaluation of material.

Carbonylation of milk powder proteins as a consequence of processing conditions

During industrial treatments, milk proteins could be oxidatively modified, thus leading to the formation of modified/oxidised amino acid residues. The apparition of such modified residues may contribute to the formation of new immunologically reactive structures. Some of these adducts could, in an advanced stage, lead to cross-linked protein species whose proteolytic susceptibility would be drastically decreased. Such protein species, that are resistant to digestion, could also constitute major food allergens. Therefore, these oxidative protein modifications tend to increase the natural allergenicity of milk proteins. For these reasons, monitoring milk protein oxidative modifications could be very useful regarding both product quality and allergenicity issues. In the present paper, we highlight, using different analytical approaches, the preferential carbonylation of beta-lactoglobulin (beta-Lg) during industrial treatments of milk. This result is particularly interesting since native beta-Lg represents one of the major milk allergens.

Covalent modification of actin by 4-hydroxy-trans-2-nonenal (HNE): LC-ESI-MS/MS evidence for Cys374 Michael adduction

We demonstrate for the first time, by a combined mass spectrometric and computational approach, that G- and F-actin can be covalently modified by the lipid-derived aldehyde, 4-hydroxy-trans-2-nonenal, providing information on the molecular mass of modified protein and the mechanism and site of adduction.ESI-MS analysis of actin treated with different molar ratios of HNE (1 : 1 to 1 : 20) showed the formation of a protein derivative in which there was an increase of 156 Da (42028 Da) over native actin (41872 Da), consistent with the adduction of one HNE residue through Michael addition. To identify the site of HNE adduction, G- and F-actin were stabilized by NaBH(4) reduction and digested with trypsin. LC-ESI-MS/MS analysis in data-dependent scan mode of the resulting peptides unequivocally indicated that Cys374 is the site of HNE adduction. Computational studies showed that the reactivity of Cys374 residue is due to a significant accessible surface and substantial thiol acidity due to the particular microenvironment surrounding Cys374.

Identification of 4-hydroxy-2-nonenal-modified peptides within unfractionated digests using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The lipid peroxidation product 4-hydroxy-2-nonenal (HNE) is generated as a consequence of oxidative stress and can readily react with nucleophilic sites of proteins (e.g., histidine residues), mainly via a Michael addition. The formation of such lipid-protein conjugates can alter protein properties and biological functions, thus leading to highly deleterious effects. The present work describes a rapid (very limited sample preparation) and sensitive (low-femtomole range) procedure to identify HNE-modified peptides (Michael adducts) within unfractionated tryptic digests. The protocol involves the formation of dinitrophenylhydrazones of the Michael adducts, when using 2,4-dinitrophenylhydrazine as reactive matrix, followed by analysis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The hydrazone derivatives present high desorption/ionization yield and can thus be preferentially detected compared to unmodified peptides. The MALDI mass spectrum obtained is therefore drastically different from the one obtained with the classical 4-hydroxy-alpha-cyanocinnamic acid matrix. Moreover, the presence of HNE, or more generally speaking carbonylated peptides, could be highlighted by 180 mass units differences (corresponding to the dinitrophenylhydrazone moiety) between these two MALDI mass spectra. Further information (e.g., localization/identification of the modified residues, peptide sequences) could be obtained by performing MALDI postsource decay (or electrospray) MS/MS experiments on the ions of interest.

Modification of Cytochrome c by 4-hydroxy- 2-nonenal: evidence for histidine, lysine, and arginine-aldehyde adducts

4-Hydroxy-2-nonenal (4HNE), a major secondary product of lipid peroxidation, has been associated with a number of disease states involving oxidative stress. Despite the recognized importance of post-translational modification of proteins by products such as 4HNE, little is known of the modification of cytochrome c by this reagent and its analysis by mass spectrometry. The purpose of this study was to investigate the chemical interaction of 4HNE and cytochrome c, a protein essential to cellular respiration, under in vitro conditions. Isoelectric focusing of native and 4HNE-modified cytochrome c using immobilized pH gradient (IpG) strips showed a decrease in the pI of the 4HNE-modified protein suggesting modification of charged amino acids. Reaction of 4HNE with cytochrome c resulted in increases in molecular weight consistent with the addition of four 4HNE residues as determined by matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS). Samples of both native and 4HNE-modified cytochrome c were enzymatically digested and subjected to peptide mass fingerprinting using MALDI-TOF MS. Analysis of these samples using LC-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) provided sequence information that was used to determine specific residues to which the aldehyde adducted. Taken together, the data indicated that H33, K87, and R38 were modified by 4HNE. Mapping these results onto the X-ray crystal structure of native cytochrome c suggest that 4HNE adduction to cytochrome c could have significant effects on tertiary structure, electron transport, and ultimately, mitochondrial dysfunction.

Mass spectrometry for detection of 4-hydroxy-trans-2-nonenal (HNE) adducts with peptides and proteins

Despite the great technical advancement of mass spectrometry, this technique has contributed in a limited way to the discovery and quantitation of specific/precocious markers linked to free radical-mediated diseases. Unsaturated aldehydes generated by free radical-induced lipid peroxidation of polyunsaturated fatty acids, and in particular 4-hydroxy-trans-2 nonenal (HNE), are involved in the onset and progression of many pathologies such as cardiovascular (atherosclerosis, long-term complications of diabetes) and neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, and cerebral ischemia). Most of the biological effects of HNE are attributed to the capacity of HNE to react with the nucleophilic sites of proteins and peptides (other than nucleic acids), to form covalently modified biomolecules that can disrupt important cellular functions and induce mutations. By considering the emerging role of HNE in several human diseases, an unequivocal analytical approach as mass spectrometry to detect/elucidate the structure of protein-HNE adducts in biological matrices is strictly needed not only to understand the reaction mechanism of HNE, but also to gain a deeper insight into the pathological role of HNE. This with the aim to provide intermediate diagnostic biomarkers for human diseases. This review sheds focus on the "state-of-the-art" of mass spectrometric applications in the field of HNE-protein adducts characterization, starting from the fundamental early studies and discussing the different MS-based approaches that can provide detailed information on the mechanistic aspects of HNE-protein interaction. In the last decade, the increases in the accessible mass ranges of modern instruments and advances in ionization methods have made possible a fundamental improvement in the analysis of protein-HNE adducts by mass spectrometry, and in particular by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) tandem mass spectrometry. The recent developments and uses of combined analytical approaches to detect and characterize the type/site of interaction have been highlighted, and several other aspects, including sample preparation methodologies, structure elucidation, and data analysis have also been considered.

Detection of arginine dimethylated peptides by parallel precursor ion scanning mass spectrometry in positive ion mode

Dimethylation at arginine residues has been shown to be central in cellular processes such as signal transduction, transcription activation, and protein sorting. The two methyl groups are either placed symmetric or asymmetric on the zeta standing nitrogen atoms of the arginine side chain. Here, we introduce a novel method that enables the localization of dimethylarginine (DMA) residues in gel-separated proteins at a level of sensitivity of better than 1 pmol and that allows one to distinguish between the isomeric symmetric and asymmetric position of the methyl groups. The method utilizes two side-chain fragments of DMA, the dimethylammonium ion (m/z 46.06) and the dimethylcarbodiimidium ion (m/z 71.06), for positive ion mode precursor ion scanning. Dimethylcarbodiimidium ions (m/z 71.06) are produced by symmetric as well as asymmetric dimethylarginine but are observed more strongly for symmetric DMA. It is utilized here in the precursor of m/z 71 scan to indicate the presence of DMA in a peptide. The dimethylammonium ion (m/z 46.06) is specific for asymmetric DMA and is utilized here in the precursor of m/z 46 scan. The positive ion mode allows for the identification of the protein by peptide sequencing and simultaneous detection and localization of the modified residues. The analysis can be conducted on any mass spectrometer capable of precursor ion scanning. However, the high resolution of a quadrupole TOF instrument is beneficial to assign the accurate charge state of the often highly charged precursors. Using the precursor of m/z 71 scan, we found FUS/TLS and Sam68 to be DMA-containing proteins. We discovered at least 20 DMA sites in FUS/TLS. In MS/MS, we observed neutral loss of dimethylamine (m/z 45.05) from which it follows that the dimethylation in FUS/TLS is asymmetric. Monitoring in parallel the fragments m/z 46.06 and 71.06 in precursor ion scans and peptide sequencing, we identified at least nine asymmetric DMA modifications in Sam68. The parallel monitoring of fragments in precursor ion scans is a versatile tool to specify the nature of protein modifications in cases where a single fragment is not conclusive.