Nitrated Peptides Research Articles

Characterization of a novel affinity binding ligand for tyrosine nitrated peptides from a phage-displayed peptide library.

As an important post-translational modification in response to oxidative and nitrosative stress, protein tyrosine nitration is deeply involved in many physiological and pathological processes. Identifying tyrosine nitration in proteins is challenging due to its low abundance.Consequently, pre-separation and enrichment of tyrosine-nitrated peptides (TNPs) are necessary before submitting them to mass spectrometry analysis. However, the most popularly used anti-nitrotyrosine antibody pull-down method showed limitations like sequence preference and unspecific binding. Therefore, developing novel affinity purification materials for TNPs is of significance. In the present study, we screened the phage-displayed 12-mer randomized peptide library for affinity binding peptide of the synthetic standard TNP (sTNP, sequence: H2N-GGGGY*GGG-COOH) and identified a peptide named NT-1 (H2N-TLWPFDLWLKTR-COOH) as a promising candidate. NT-1 at extremely low concentration (3nM) in solutions could be efficiently captured by immobilized sTNP as determined by pull-down and subsequent MALDI-TOF MS analysis. Surface plasmon resonance (SPR) measurement confirmed that NT-1 possesseed a good selectivity, showing more than 100-fold higher binding affinity with TNP than its non-nitrated counterpart. Moreover, NT-1 could efficiently capture various types of TNPs in solutions even in the presence of 1000-fold excessive amount of trypsinized BSA fragments. Most importantly, NT-1 showed superiority to commercially used nitrotyrosine antibody as the former captured more TNPs, with less sequence preference. In summary, our study provided NT-1 as a novel affinity binding ligand for TNPs and should be useful in developing an alternative enrichment strategy for TNPs.

RPTMDetermine: A Fully Automated Methodology for Endogenous Tyrosine Nitration Validation, Site-Localization, and Beyond.

We present herein rPTMDetermine, an adaptive and fully automated methodology for validation of the identification of rarely occurring post-translational modifications (PTMs), using a semisupervised approach with a linear discriminant analysis (LDA) algorithm. With this strategy, verification is enhanced through similarity scoring of tandem mass spectrometry (MS/MS) comparisons between modified peptides and their unmodified analogues. We applied rPTMDetermine to (1) perform fully automated validation steps for modified peptides identified from an in silico database and (2) retrieve potential yet-to-be-identified modified peptides from raw data (that had been missed through conventional database searches). In part (1), 99 of 125 3-nitrotyrosyl-containing (nitrated) peptides obtained from a ProteinPilot search were validated and localized. Twenty nitrated peptides were falsely assigned because of incorrect monoisotopic peak assignments, leading to erroneous identification of deamidation and nitration. Five additional nitrated peptides were, however, validated after performing nonmonoisotopic peak correction. In part (2), an additional 236 unique nitrated peptides were retrieved and localized, containing 113 previously unreported nitration sites; 25 endogenous nitrated peptides with novel sites were selected and verified by comparison with synthetic analogues. In summary, we identified and confidently validated 296 unique nitrated peptides-collectively representing the largest number of endogenously identified 3-nitrotyrosyl-containing peptides from the cerebral cortex proteome of a Macaca fascicularis model of stroke. Furthermore, we harnessed the rPTMDetermine strategy to complement conventional database searching and enhance the confidence of assigning rarely occurring PTMs, while recovering many missed peptides. In a final demonstration, we successfully extended the application of rPTMDetermine to peptides featuring tryptophan oxidation.

THU0098 ANTIBODIES AGAINST THREE POST-TRANSLATIONAL PROTEIN MODIFICATIONS IN PATIENTS WITH RHEUMATOID ARTHRITIS

Background:Autoantibodies to some post-translational modifications (PTMs) of proteins have a relevant role in rheumatoid arthritis (RA). Antibodies to other PMTs such as carbonylation (aCarbo) [1], nitration (aNitra) [2] and homocysteinylation (aHCis) [3] have also been described but they have been scarcely studied.Objectives:We aimed to evaluate the presence of antibodies against three poorly studied PTMs in patients with RA and explore their value as biomarkers.Methods:Serum samples from 196 healthy controls and RA patients meeting the 1987 ACR classification criteria that had either early RA (< 2 years from symptom onset) (n=182) or established RA (n=143) were analyzed. The antibodies were evaluated by indirect ELISA following the described protocols [1-3]. They include as antigens: HOCl- or ribose- carbonylated bovine type II collagen (HOCl-CII and GLI-CII, respectively) for aCarbo antibodies; homocysteinylated human serum albumin (Hcy-HSA) for aHCis antibodies; andin vitronitrated synovial proteins and synthetic nitrated peptides (3-NT-PS and 3-NT-pep, respectively) for aNitra antibodies. The efficiency of the reactions to produce these PTMs was verified. The study was approved by the CEIC of Galicia. The results were analyzed as differences between the optical densities (OD) obtained without correction, or the specific OD after subtracting reactivity to the native protein.Results:The aCarbo antibodies were studied in patients with early RA, as reported [1]. Despite this, uncorrected ODs against the two carbonylated forms of CII were not greater in the patients than in the controls (Table 1). Consequently, the corrected reactivity to GLI-CII that was significantly higher in patients than controls did not reflect aCarbo antibodies but differences in reactivity to native bovine CII.The other antibodies were analyzed in patients with established RA as previously done [2,3]. However, none of them showed specific reactivity (Table 1). In effect, although an excess of uncorrected reactivity to 3-NT-pep was observed in the patients with RA, it disappeared when corrected (Table 1). Also, the vast majority of patients and controls showed no reactivity to 3-NT-SP (not shown). In turn, the aHCis antibodies were significantly elevated in patients, but only in the uncorrected analysis because the difference disappeared when corrected for reactivity against native HSA (Table 1).Table 1.Antibodies against three post-translational protein modifications in RA patients and controlsRAControlsAntigenCorrectionMedian DOIQRMedian DOIQRPHOCl-CIIno0.1410.127/0.1730.1600.141/0.1880.0001HOCl-CIIyes-0.003-0.011/0.008-0.004-0.020/0.0050.02GLI-CIIno0.2340.171/0.2850.2220.163/0.3050.5GLI-CIIyes0.0720.016/0.1150.028-0.010/0.1000.00053-NT-pepno0.2500.201/0.3290.2090.190/0.2300.023-NT-pepyes0.1370.097/0.1850.1130.100/0.1330.1Hcy-HSAno0.1600.145/0.1780.1450.130/0.1550.00011Hcy-HSAyes-0.041-0.074/-0.015-0.038-0.069/-0.200.5Conclusion:The presence in RA patients of specific antibodies against the three PTMs has not been replicated. None of the observed reactivities were attributable to the PTMs. If confirmed, these results would indicate that only particular PTMs are relevant for RA and that carbonylation, nitration or homocysteinylation are not among them.

Binding Affinities Studies of Nitrated Model Peptides to Monoclonal Anti-3-nitrotyrosine Antibody

Tyrosine nitration has been shown to be an important oxidative protein modification and play a crucial role in pathophysiological conditions, associated with oxidative stress, such as atherosclerosis and neurodegenerative disease. For a better understanding of nitration mechanism, the identification and the quantification of nitration sites represents an important research goal. Due to (i) the low levels of nitration in native proteins, (ii) structural changes induced by nitration and (iii) the specificity of anti � 3 nitro tyrosine antibodies the method which may provide the identification of nitration sites in proteins represent a challenging experimental task. In this work we have used synthetic nitrated tyrosine containing peptides to determine antibody-binding affinities and specificity of different tyrosine residue (Tyr33, Tyr98, Tyr107and Tyr122) in Eosinophil cationic proteins (ECP). The highest affinity of nitrated ECP peptides to the monoclonal antibody (anti-3NT) was obtained for the only in vivo nitrated identified residue Tyr33(0.082 �M); in contrast, all other three nitrated residues at Tyr98, Tyr107 and Tyr122) showed significant lower affinity being imbedded in the ECP protein structure as similar resulted by molecular computational modeling.

Fully automated multidimensional reversed-phase liquid chromatography with tandem anion/cation exchange columns for simultaneous global endogenous tyrosine nitration detection, integral membrane protein characterization, and quantitative proteomics mapping in cerebral infarcts.

Protein tyrosine nitration (PTN) is a signature hallmark of radical-induced nitrative stress in a wide range of pathophysiological conditions, with naturally occurring abundances at substoichiometric levels. In this present study, a fully automated four-dimensional platform, consisting of high-/low-pH reversed-phase dimensions with two additional complementary, strong anion (SAX) and cation exchange (SCX), chromatographic separation stages inserted in tandem, was implemented for the simultaneous mapping of endogenous nitrated tyrosine-containing peptides within the global proteomic context of a Macaca fascicularis cerebral ischemic stroke model. This integrated RP-SA(C)X-RP platform was initially benchmarked through proteomic analyses of Saccharomyces cerevisiae, revealing extended proteome and protein coverage. A total of 27 144 unique peptides from 3684 nonredundant proteins [1% global false discovery rate (FDR)] were identified from M. fascicularis cerebral cortex tissue. The inclusion of the S(A/C)X columns contributed to the increased detection of acidic, hydrophilic, and hydrophobic peptide populations; these separation features enabled the concomitant identification of 127 endogenous nitrated peptides and 137 transmembrane domain-containing peptides corresponding to integral membrane proteins, without the need for specific targeted enrichment strategies. The enhanced diversity of the peptide inventory obtained from the RP-SA(C)X-RP platform also improved analytical confidence in isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analyses.

A novel targeted proteomics method for identification and relative quantitation of difference in nitration degree of OGDH between healthy and diabetic mouse.

For analysis of nitration modification of α oxoglutarate dehydrogenase (α-OGDH) induced by diabetes, a targeted proteomics strategy was developed through the use of Skyline. All peptides containing Y and W of the target proteins were nitrated in silico and output to produce parallel reaction monitoring (PRM) or SRM method for nitration analysis. A nitrated casein mixture was used as standard protein to assess the feasibility of this method. The results demonstrated the availability of this strategy for nitration identification, and subsequently this method was used to analyze the nitration of α-OGDH from myocardial tissue extracts of diabetic mouse. The PRM method was primarily generated by Skyline for identification of the actual nitrated peptides from all possible nitrated peptides of α-OGDH due to the complexity of α-OGDH. The PRM-based data were analyzed by SEQUEST, and transitions of the identified nitrated peptides were used to develop an SRM method for relative quantitation of nitration degree. The nitration degree of α-OGDH for diabetic mouse is higher than that for control mouse, indicating that α-OGDH of the diabetic mouse suffered from more intense oxidative damage. We believe that this approach for obtaining information regarding nitration will facilitate the study of other PTMs in complex mixtures.

Monitoring succinyl-CoA:3-oxoacid CoA transferase nitration in mitochondria using monoclonal antibodies

Two tyrosine residues (Tyr4 and Tyr76) of succinyl-CoA:3-oxoacid CoA transferase (SCOT) are sensitive to nitric oxide (NO) stress, as assessed by mass spectrometry and site-direct mutagenesis. However, monitoring the SCOT nitration in tissue or cells is challenging. Herein, we describe the development of an assay to detect nitrated SCOT directly using site-specific antibodies; the monoclonal antibodies were generated and screened against nitrated peptides of SCOT. After stringent filtration, two antibodies, anti-SCOT4N and anti-SCOT76N, which specifically recognise Tyr4 or Tyr76 of SCOT, respectively, were successfully selected. In a cell model over-expressing iNOS in the mitochondria, nitrated SCOT was significantly increased compared with control cells. In addition, in a mouse model of diabetes, nitrated Tyr4 and Tyr76 in the heart and kidney were higher compared to the control animals. Our results using monoclonal antibodies against nitrated SCOT peptides are in good agreement with the proteomic data.

Identification of Nitrotyrosine Containing Peptides using Combined Fractional Diagonal Chromatography (COFRADIC) and Off-Line Nano-LC-MALDI

Protein nitration take place on tyrosine residues under oxidative stress conditions and may influence a number of processes including enzyme activity, protein-protein interactions and phospho-tyrosine signalling pathways. Nitrated proteins have been identified in a number of diseases, however, the study of these proteins has been compromised by the lack of good methods for identifying nitrated proteins, their nitration sites and the level of nitration. Here, we present a method for identification of nitrated peptides that allows the site specific assignment of nitration, is easy to use and reproducible, and opens up for the possibility to quantify the level of nitration of specific peptides as function of different oxidative conditions, namely combined fractional diagonal chromatography (COFRADIC) in combination with off-line nano-LC-MALDI. We identify six nitrated peptides from in vitro nitrated bovine serum albumin and propose that automated COFRADIC using nano-LC and off-line MALDI-MS might be a possibility for identification of tyrosine nitrated proteins and the nitration sites in complex samples.

In vivo protein tyrosine nitration in Arabidopsis thaliana

Nitration of tyrosine (Y) residues of proteins is a low abundant post-translational modification that modulates protein function or fate in animal systems. However, very little is known about the in vivo prevalence of this modification and its corresponding targets in plants. Immunoprecipitation, based on an anti-3-nitroY antibody, was performed to pull-down potential in vivo targets of Y nitration in the Arabidopsis thaliana proteome. Further shotgun liquid chromatography–mass spectrometry (LC-MS/MS) proteomic analysis of the immunoprecipitated proteins allowed the identification of 127 proteins. Around 35% of them corresponded to homologues of proteins that have been previously reported to be Y nitrated in other non-plant organisms. Some of the putative in vivo Y-nitrated proteins were further confirmed by western blot with specific antibodies. Furthermore, MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) analysis of protein spots, separated by two-dimensional electrophoresis from immunoprecipitated proteins, led to the identification of seven nitrated peptides corresponding to six different proteins. However, in vivo nitration sites among putative targets could not be identified by MS/MS. Nevertheless, an MS/MS spectrum with 3-aminoY318 instead of the expected 3-nitroY was found for cytosolic glyceraldehyde-3-phosphate dehydrogenase. Reduction of nitroY to aminoY during MS-based proteomic analysis together with the in vivo low abundance of these modifications made the identification of nitration sites difficult. In turn, in vitro nitration of methionine synthase, which was also found in the shotgun proteomic screening, allowed unequivocal identification of a nitration site at Y287.

Selective Enrichment and Mass Spectrometric Identification of Nitrated Peptides Using Fluorinated Carbon Tags

Protein tyrosine nitration (PTN) is a post-translational modification that is related to several acute or chronic diseases. PTN introduces a nitro group in the ortho position of the phenolic hydroxyl group of tyrosine residues. PTN has been shown to be involved in the pathogenesis of inflammatory responses, cancers, and neurodegenerative and age-related disorders. Furthermore, it has been proposed that PTN regulates signal cascades related to nitric oxide (NO·) production and NO-mediated processes. Although nitrated proteins as markers of oxidative stress are confirmed by immunological assays in various affected cells or tissues, it is not known how many different types of proteins in living cells are nitrated. Since protein nitration is a low-abundance post-translational modification, development of an effective enrichment method for nitrated proteins is needed to detect nitrated peptides or proteins from the limited amount of pathophysiological samples. In the present study, we developed an enrichment method using specific chemical tagging. Nitroproteome profiling using chemical tagging and mass spectrometry was validated by model proteins. Furthermore, we successfully identified numerous nitrated proteins from the Huh7 human hepatoma cell line.

Mass spectrometric characterization of photooxidative protein modifications in Arabidopsis thaliana thylakoid membranes

Oxidative and nitrosative stress leaves footprints in the plant chloroplast in the form of oxidatively modified proteins. Using a mass spectrometric approach, we identified 126 tyrosine and 12 tryptophan nitration sites in 164 nitrated proteolytic peptides, mainly from photosystem I (PSI), photosystem II (PSII), cytochrome b(6) /f and ATP-synthase complexes and 140 oxidation products of tyrosine, tryptophan, proline, phenylalanine and histidine residues. While a high number of nitration sites were found in proteins from four photosynthetic complexes indicating that the nitration belongs to one of the prominent posttranslational protein modifications in photosynthetic apparatus, amino acid oxidation products were determined mostly in PSII and to a lower extent in PSI. Exposure of plants to light stress resulted in an increased level of tyrosine and tryptophan nitration and tryptophan oxidation in proteins of PSII reaction center and the oxygen-evolving complex, as compared to low light conditions. In contrast, the level of nitration and oxidation of these amino acid residues strongly decreased for all light-harvesting proteins of PSII under the same conditions. Based on these data, we propose that oxidative modifications of proteins by reactive oxygen and nitrogen species might represent an important regulatory mechanism of protein turnover under light stress conditions, especially for PSII and its antenna proteins.

Top-down mass analysis of protein tyrosine nitration: comparison of electron capture dissociation with "slow-heating" tandem mass spectrometry methods.

Tyrosine nitration in proteins is an important post-translational modification (PTM) linked to various pathological conditions. When multiple potential sites of nitration exist, tandem mass spectrometry (MS/MS) methods provide unique tools to locate the nitro-tyrosine(s) precisely. Electron capture dissociation (ECD) is a powerful MS/MS method, different in its mechanisms to the “slow-heating” threshold fragmentation methods, such as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). Generally, ECD provides more homogeneous cleavage of the protein backbone and preserves labile PTMs. However recent studies in our laboratory demonstrated that ECD of doubly charged nitrated peptides is inhibited by the large electron affinity of the nitro group, while CID efficiency remains unaffected by nitration. Here, we have investigated the efficiency of ECD versus CID and IRMPD for top-down MS/MS analysis of multiply charged intact nitrated protein ions of myoglobin, lysozyme, and cytochrome c in a commercial Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. CID and IRMPD produced more cleavages in the vicinity of the sites of nitration than ECD. However the total number of ECD fragments was greater than those from CID or IRMPD, and many ECD fragments contained the site(s) of nitration. We conclude that ECD can be used in the top-down analysis of nitrated proteins, but precise localization of the sites of nitration may require either of the “slow-heating” methods.

Probing the mechanisms of electron capture dissociation mass spectrometry with nitrated peptides.

Previously we have shown that the presence of 3-nitrotyrosine within a peptide sequence severely depletes the peptide backbone fragments typically observed following electron capture dissociation (ECD) mass spectrometry. Instead, ECD of nitrated peptides is characterised by abundant losses of small neutrals (hydroxyl radicals, water and ammonia). Here, we investigate the origin of ammonia loss by comparing the ECD behaviour of lysine- and arginine-containing nitrated peptides, and their N-acetylated counterparts, and nitrated peptides containing no basic amino acid residues. The results reveal that ammonia loss derives from the N-terminus of the peptides, however, the key finding of this work is the insight provided into the hierarchy of various proposed ECD mechanisms: the Utah-Washington mechanism, the electron predator mechanism and the Oslo mechanism.

Efficient Identification and Quantification of Peptides Containing Nitrotyrosine by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry after Derivatization

Protein nitration at tyrosine residues proceeds to form 3-nitrotyrosine; this product is today used as a biomarker of nitrative stress. We have developed an efficient method with which to identify nitrated peptides and to quantify protein nitration levels in different biological samples by a combination of the chemical derivatization of nitrotyrosine-containing peptides and mass spectrometry. Our strategy includes: 1) the protection of both N-terminal amines and epsilon-amines of lysine residues by acetylation with (13)C(0)/(13)C(4)- or D(0)/D(6)-acetic anhydride; 2) the reduction of nitrotyrosine to aminotyrosine with sodium hydrosulfite; and 3) the derivatization of aminotyrosine with 1-(6-methyl[D(0)/D(3)]nicotinoyloxy)succinimide. The utility of our method is demonstrated with nitrotyrosine-containing angiotensin II and bovine serum albumin as the model compounds.

Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.

Chemical Approach for Specific Enrichment and Mass Analysis of Nitrated Peptides

The analysis and detection of 3-nitrotyrosine are biologically and clinically important because protein tyrosine nitration is known to be involved in a number of biological phenomena such as cellular signal transduction, pathogenesis of inflammatory responses, and age-related disorders. However, the main obstacles in the study are low abundance of nitrated species and lack of efficient enrichment methods. Here in, we suggest a new chemical approach to analyze nitrated peptides using mass spectrometry by incorporating specific tagging groups in the peptides through simple chemical transformations. Nitro groups on tyrosine side chains of nitrated peptides were subjected to reduction to give rise to amine which was further converted to metal-chelating motif. Mass analyses verified that Ni(2+)-NTA magnetic agarose beads selectively captured and isolated the modified peptides, i.e., nitrated peptides, by strong and specific metal chelating interactions. We further demonstrated the utility of our approach by detection of nitrated peptides in complex samples such as tryptic peptide mixtures of bovine serum albumin (BSA) and a HeLa cell lysate.

Enhanced Nitrosative Stress during Trypanosoma cruzi Infection Causes Nitrotyrosine Modification of Host Proteins : Implications in Chagas' Disease

Oxidative/nitrosative stress may be important in the pathology of Chagas' disease. Experimental animals infected by Trypanosoma cruzi showed an early rise in myocardial and peripheral protein-3-nitrotyrosine (3NT) and protein-carbonyl formation that persisted during the chronic stage of disease. In comparison, experimental chronic ethanol-induced cardiomyopathy was slow to develop and presented with a moderate increase in oxidative stress and minimal to no nitrosative stress after long-term alcohol feeding of animals. The oxidative stress in both chagasic animals and animals with ethanol-induced cardiomyopathy correlated with the persistence of reactive oxygen species-producing inflammatory intermediates. Protein-3NT formation in T. cruzi-infected animals was associated with enhanced nitric oxide expression (inferred by nitrite/nitrate levels) and myeloperoxidase activity, suggesting that both peroxynitrite- and myeloperoxidase-mediated pathways contribute to increased protein nitration in Chagas' disease. We used one- and two-dimensional gel electrophoresis and Western blot analysis to identify disease-specific plasma proteins that were 3NT-modified in T. cruzi-infected animals. Nitrated protein spots (56 in total) were sequenced by matrix-assisted laser desorption ionization/time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry and identified by a homology search of public databases. Clustering of 3NT-modified proteins according to their functional characteristics revealed that the nitration of immunoglobulins, apolipoprotein isoforms, and other proteins might perturb their functions and be important in the pathology of Chagas' disease. We also showed that nitrated peptides derived from titin and alpha-actin were released into the plasma of patients with Chagas' disease. Such modified proteins may be useful biomarkers of Chagas' disease.

A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples

Elevated levels of protein tyrosine nitration have been found in various neurodegenerative diseases and age-related pathologies. Until recently, however, the lack of an efficient enrichment method has prevented the analysis of this important low-level protein modification. We have developed a method that specifically enriches nitrotyrosine-containing peptides so that both nitrotyrosine peptides and specific nitration sites can be unambiguously identified with LC-MS/MS. The procedure consists of the derivatization of nitrotyrosine into free sulfhydryl groups followed by high efficiency enrichment of sulfhydryl-containing peptides with thiopropyl sepharose beads. The derivatization process includes: (1) acetylation with acetic anhydride to block all primary amines, (2) reduction of nitrotyrosine to aminotyrosine, (3) derivatization of aminotyrosine with N-Succinimidyl S-Acetylthioacetate (SATA), and (4) deprotection of S-acetyl on SATA to form free sulfhydryl groups. The high specificity of this method is demonstrated by the contrasting percentage of nitrotyrosine-derivatized peptides in the identified tandem mass spectra between enriched and unenriched samples. Global analysis of unenriched in vitro nitrated human histone H1.2, bovine serum albumin (BSA), and mouse brain homogenate samples had 9%, 9%, and 5.9% of identified nitrotyrosine-containing peptides, while the enriched samples had 91% , 62%, and 35%, respectively. Duplicate LC-MS/MS analyses of the enriched mouse brain homogenate identified 150 unique nitrated peptides covering 102 proteins with an estimated 3.3% false discovery rate.

Improved tandem mass spectrometric characterization of 3‐nitrotyrosine sites in peptides

Nitrated tyrosines are easily converted into their aminotyrosine equivalents by a reduction step. We here show that this conversion can be exploited to readily discern 3-aminotyrosine peptides in a background of non-nitrated peptides. Furthermore, aminotyrosine peptides are more stable in single mass spectrometry (MS) mode rendering peptide mass maps easier to interpret. One significant caveat of both 3-nitrotyrosine and 3-aminotyrosine peptides is their lack of efficient fragmentation upon collision-induced dissociation (CID) which, in the case of the latter peptides, also produces unexpected, deviating isotopic patterns of fragment ions containing the aminotyrosine residue. The net result is that sequence database searching becomes daunting as the correct peptide is frequently missed since insufficient and/or inaccurate peptide fragments are used. We show that a simple acetylation step, blocking all amines (including aminotyrosine), produces peptides that undergo extensive backbone fragmentation by CID and are thus easily identifiable in databases. Our procedure is additionally illustrated by doubling the number of nitration events mapped in tetranitromethane-nitrated bovine serum albumin (BSA) as compared to a direct analysis of the nitrated peptides using the same amount of material. In conclusion, we here illustrate that this two-step process, heme-mediated reduction and acetylation, can be used for more efficient characterization of protein-bound nitrated tyrosines.

3-Nitrotyrosine Modification of SERCA2a in the Aging Heart: A Distinct Signature of the Cellular Redox Environment

In the aging heart, decreased rates of calcium transport mediated by the SERCA2a isoform of the sarcoplasmic reticulum (SR) Ca-ATPase are responsible for the slower sequestration of cytosolic calcium and consequent prolonged muscle relaxation times. We report a 60% decrease in Ca-ATPase activity in the senescent Fischer 344 rat heart relative to that of young adult hearts; this functional decrease can be attributed, in part, to the 18% lower abundance of SERCA2a protein. Here, we show that the additional loss of activity is a result of increased 3-nitrotyrosine modification of the Ca-ATPase. Age-dependent increases in nitration of cardiac SERCA2a are identified using multiple analytical methods. In the young (adult) heart 1 molar equivalent of nitrotyrosine is distributed over at least five tyrosines within the Ca-ATPase, identified as Tyr(122), Tyr(130), Tyr(497), Tyr(586), and Tyr(990). In the senescent heart, the stoichiometry of nitration increases by more than two nitrotyrosines per Ca-ATPase, coinciding with the appearance of nitrated Tyr(294), Tyr(295), and Tyr(753). The abundant recovery of native analogues for each of the nitrated peptides indicates partial modification of multiple tyrosines within cardiac SERCA2a. In contrast, within skeletal muscle SERCA2a, a homogeneous pattern of nitration appears, with full site (1 mol/mol) nitration of Tyr(753), in young, with additional nitration of Tyr(294) and Tyr(295), in senescent muscle. The nitration of these latter vicinal sites correlates with diminished transport function in both striated muscle types, suggesting that these sites provide a mechanism for downregulation of ATP utilization by the Ca-ATPase under conditions of nitrative stress.