Binding sites of [Ru(bpy)2(H2O)2](BF4)2 with sulfur- and histidine-containing peptides studied by electrospray ionization mass spectrometry and tandem mass spectrometry

The composition and binding sites of cis-[Ru(II)(bpy)2]2+-bound sulfur-containing peptides of Met-Arg-Phe-Ala, glutathione and oxidized glutathione, and also histidine-containing peptide of oxidized insulin B chain, were investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). The composition of Ru(II)-containing peptides was precisely determined by ESI-MS, zoom scan and simulation of isotope distribution patterns. MS/MS analysis shows that, in sulfur-containing peptides, the Ru(II) complex prefers to anchor to a carboxyl group, although some other potential binding sites of thiol, thioether and N-terminal amino groups present in these peptides, and in oxidized insulin B chain, Ru(II) first anchors to His10, then either to the hydroxyl group of Thr27 or to the carboxyl group of Ala30. Its secondary structure and microenvironment surrounding the potential binding sites may affect the binding ability of cis-[Ru(II)(bpy)2]2+ to oxidized insulin B chain.     

Amino acid and peptide conjugates of protoporphyrin: preparation and analysis by high-performance liquid chromatography,high-performance liquid chromatography/electrospray ionization mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Amino acid and peptide conjugates of protoporphyrin have been prepared by reacting protoporphyringen with cysteine, glutathione and peptides containing a free thiol group under acidic conditions. The conjugates were formed by the addition of the thioamino acids or peptides to the vinyl groups of protoporphyrin during the autoxidation of protoporphyinogen to protoporphyrin and is free-radical-mediated. The conjugates were separated by high-performance liquid chromatography (HPLC) and characterized by HPLC/electrospray ionization mass spectrometry (HPLC/ESI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). All the conjugates formed were diconjugates consisting of diastereoisomers.     

Methylating peptides to prevent adduct ion formation also directs cleavage in collision-induced dissociation mass spectrometry

We investigated the effect of N-terminal amino group and carboxyl group methylation on peptide analysis by electrospray mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS/MS). Permethylation of the N-terminal amino group and the carboxyl groups can reduce metal ion adducts but does not enhance sensitivity in electrospray as previously observed for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. N-terminal trimethylated peptides exhibit collision-induced dissociation (CID) tandem mass spectra that differ from their unmodified analogs; the results support the mobile proton hypothesis of peptide fragmentation. A permanent positive charge at the N-terminus leads to competition between permanent-charge directed processes and loss of the N-terminal trimethyl amino group. Carboxyl methylation has no effect on fragmentation behavior other than to shift the mass of fragments containing methylated carboxyl groups. Comparison of regular and tandem mass spectra of different methylated peptides allowed probing the location of incomplete methylation, the proton displaced by alkali metal ions and the purity of a mass-selected methylated peptide ion.     

Structural analysis of naphthoquinone protein adducts with liquid chromatography/tandem mass spectrometry and the scoring algorithm for spectral analysis (SALSA)

The relative reactivities of various naphthoquinone isomers (1,4-, 1,2- and 2-methyl-1,4-naphthoquinone) to two test proteins, apomyoglobin and human hemoglobin, were evaluated via liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS). The structural characterization of the resulting adducts was also obtained by LC/ESI-MS analysis of the intact proteins. The reactive sites of apomyoglobin and human hemoglobin with 1,4-naphthoquinone and 1,2-naphthoquinone were also identified through characterization of adducted tryptic peptides by use of high-pressure liquid chromatography/electrospray ionization with tandem mass spectrometry (HPLC/ESI-MS/MS), TurboSEQUEST, and the scoring algorithm for spectral analysis (SALSA). Four adducted peptides, which were formed by nucleophilic addition of a lysine amino acid residue to 1,4-naphthoquinone, were also identified, as was an adducted peptide from incubation of 1,2-naphthoquinone with apomyoglobin. In the case of incubation of human hemoglobin with the two naphthoquinones, two adducted peptides were identified from the N-terminal valine modification of the alpha and beta chains of human hemoglobin. The adducted protein formation may imply that naphthalene produces its in vivo toxicity through 1,2- and 1,4-naphthoquinone metabolites reacting with biomolecular proteins.     

Differential labeling of free and disulfide-bound thiol functions in proteins

A method for the simultaneous determination of the number of free cysteine groups and disulfide-bound cysteine groups in proteins has been developed based on the sequential labeling of free and bound thiol functionalities with two ferrocene-based maleimide reagents. Liquid chromatography/electrochemistry/mass spectrometry was used to assign the N-(2-ferroceneethyl)maleimide (FEM) labeled free cysteine functionalities in a tryptic digest mixture, whereas a precursor ion scan enables the detection of peptides with ferrocenecarboxylic acid-(2-maleimidoyl)ethylamide (FMEA) labeled disulfide-bound cysteine groups after reduction. Fragment spectra of the labeled peptides yield an excellent coverage of b-type and y-type ions. The ferrocene labeled cysteines were fragmented as 412 Da (FEM) and 455 Da (FMEA). These fragment masses are significantly higher than unlabeled amino acids or dipeptides and are easily detected. The position of free and disulfide-bound cysteine may therefore be assigned in an amino acid sequence.     

产物可用电喷雾质谱检测的氨基酸/肽季铵化新方法

氨基酸和肽中氨基的化学修饰反应,如乙酰化反应和烷基化反应已被广泛用于蛋白组学研究中蛋白质的定量分析．氨基酸和肽的季铵化产物具有独特的优点,在电喷雾质谱中具有很好的离子化效率,可大大提高检测的灵敏度．文献[6～8]报道的氨基酸和肽的季铵化方法均使用高浓度的盐(如KHCO3),严重影响了质谱的检测结果,难以直接用于蛋白质组学研究．     

Counting sulfhydryls and disulfide bonds in peptides and proteins using mercurial ions as an MS-tag

Organic mercurial compounds are the most specific and sensitive reagents for reaction with the sulfhydryl groups (SHs) in peptides and proteins because of the strong mercury-sulfur affinity. Using the monofunctional organic mercury ion RHg(+) as a mass spectrometry (MS)-tag has the advantages of reacting with one sulfhydryl group, offering definite mass shift, and especially stable and characteristic nonradioactive isotopic distribution. Mass spectrometric analysis of derivatized sulfhydryls in peptides/proteins is thus an alternative for precisely counting the number of sulfhydryl groups and disulfide bonds (SS). Here the tags used include monomethylmercury chloride, monoethylmercury chloride, and 4-(hydroxymercuri) benzoic acid. The feasibility of this strategy is demonstrated using HPLC/ESI-MS to count SHs and SS in model peptides/proteins, i.e., glutathione, phytochelatins, lysozyme and beta-lactoglobulin, which contain increasing SHs and various SS linkages.     

Michael addition of acrolein to lysinyl and N-terminal residues of a model peptide: targets for cytoprotective hydrazino drugs

The antihypertensive drug hydralazine blocks acrolein-mediated toxicity by trapping both free aldehyde- and acrolein-adducted proteins, with the latter property more closely related to cytoprotection in cellular models. Here we report the identification of products from 'protein adduct-trapping' reactions using electrospray ionisation mass spectrometry (ESI-MS). Reaction of a 13-residue peptide containing a single lysine with acrolein for 30 min generated ions corresponding to mono- and bis-Michael-adducted peptides. An ion corresponding to a cyclic species formed from bis-adducted lysine was conspicuous at later times (60, 180 min). Tandem mass spectrometric (MS/MS) analysis revealed Michael adduction also occurred on the N-terminus, with a novel N-terminal (3-formyl-3,4-dehydropiperidino) species formed on this residue. Addition of hydralazine to acrolein-adducted peptides generated a diverse range of hydrazones that were also characterised by MS/MS analysis. The results confirm that mass spectrometry is a powerful tool for characterising the reactions of noxious electrophiles with biological macromolecules.     

Negative-ion electrospray ionization tandem mass spectrometry of N-phosphoryl amino acids and dipeptides

The negative-ions of N-phosphoryl amino acids were studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The negative-ion ESI-MS/MS of N-phosphoryl amino acids showed characteristic fragmentation patterns different from those observed in the corresponding positive-ion ESI-MS/MS and negative-ion fast-atom bombardment mass spectra. For negative-ion ESI-MS/MS, a unique fragmentation from the N-terminal of N-phosphoryl amino acids or peptides containing a free beta-OH or CO(2)H group was observed to yield the characteristic fragment ion (RO)(2)P(O)O(-). The ease of the rearrangement depended on the position of the hydroxyl group in amino acids or peptides, and the N --> O rearrangement mechanism was proposed to involve the participation of the hydroxyl group. From previous solution-phase experiments and theoretical calculations, it was found that the beta-OH group was more active than gamma-OH, and the corresponding difference in negative-ion ESI-MS/MS was consistent with those previous findings.     

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.     

Novel synthetic method of phosphonamidate peptides and its application in peptide sequencing via multistage mass spectrometry

Phosphonamidate peptides were prepared in good yields by reaction of ethoxy(phenyl)phosphinate with free peptides in a mixed solution of H2O, C2H5OH, Et3N and CCl4 at room temp.; their in situ electrospray ionization mass spectra exhibited high sensitivity compared with the free peptides, and sequential loss of amino acid residues of the sodiated phosphonamidate peptides from the C-terminus was found in multistage ESI mass spectrometry. The results show that N-phosphonyl derivatization combined with multistage ESI-MS is a powerful method for peptide sequencing.     

Characterizing closely spaced, complex disulfide bond patterns in peptides and proteins by liquid chromatography/electrospray ionization tandem mass spectrometry

Identifying the Cys residues involved in disulfide linkages of peptides and proteins that contain complex disulfide bond patterns is a significant analytical challenge. This is especially true when the Cys residues involved in the disulfide bonds are closely spaced in the primary sequence. Peptides and proteins that contain free Cys residues located near disulfide bonds present the additional problem of disulfide shuffling via the thiol-disulfide exchange reaction. In this paper, we report a convenient method to identify complex disulfide patterns in peptides and proteins using liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with partial reduction by tris(2-carboxyethyl)phosphine (TCEP). The method was validated using well-characterized peptides and proteins including endothelin, insulin, alpha-conotoxin SI and immunoglobulin G (IgG2a, mouse). Peptide or protein digests were treated with TCEP in the presence of an alkylation reagent, maleimide-biotin (M-biotin) or N-ethylmaleimide (NEM), followed by complete reduction with dithiothreitol and alkylation by iodoacetamide (IAM). Subsequently, peptides that contained alkylated Cys were analyzed by capillary LC/ESI-MS/MS to determine which Cys residues were modified with M-biotin/NEM or IAM. The presence of the alkylating reagent (M-biotin or NEM) during TCEP reduction was found to minimize the occurrence of the thiol-disulfide exchange reaction. A critical feature of the method is the stepwise reduction of the disulfide bonds and the orderly, sequential use of specific alkylating reagents.     

Probing of arginine residues in peptides and proteins using selective tagging and electrospray ionization mass spectrometry

A general labelling method is presented which allows the determination of the number of guanidine groups (related to arginine and homoarginine in peptides and proteins) by means of mass spectrometry. It implies a guanidine-selective derivatization step with 2,3-butanedione and an arylboronic acid under aqueous, alkaline conditions (pH 8-10). The reaction mixture is then directly analysed by electrospray ionization mass spectrometry without further sample pretreatment. Other amino acids are not affected by this reaction although it is demonstrated that lysine side-chains may be unambiguously identified when they are converted to homoarginine prior to derivatization. Guanidine functionalities, as e.g. in the amino acid arginine, are easily identified by the characteristic mass shift between underivatized and derivatized analyte. The tagging procedure is straightforward and selective for guanidine groups. The influence of several experimental parameters, especially the pH of the solution and the choice of reagents, is examined and the method is applied to various arginine-containing peptides and to lysozyme as a representative protein. Possible applications of this technique and its limitations are discussed.     

Electrospray ionization mass spectrometric studies of phosphorus oxychloride directed synthesis of homo-oligopeptide ester libraries

With the assistance of phosphorus oxychloride, alpha-amino acids were assembled into homo-peptides, which were analyzed by electrospray ionization mass spectrometry (ESI-MS) and multistage electrospray ionization mass spectrometry (ESI-MS/MS). On quenching with water or various alcohols, the reaction mixtures yielded the corresponding peptides or peptide esters, respectively. This paper reports a simple method to synthesize the homo-oligo-peptide-ester conjugated library by phosphorus oxychloride activation.     

氨基酸-磷酸非共价复合物离子的电喷雾电离质谱研究

分子间的非共价相互作用对于理解分子复合物的结构和性质有着非常重要的意义。而电喷雾电离质谱(ESI-MS)是团簇化学研究的一种重要工具,广泛用于重要生物分子复合物的形成和性质研究,包括氨基酸、多肽和核糖等。该文将一定化学剂量比的磷酸分别与L型精氨酸和L型色氨酸混合,通过电喷雾电离的方法,利用傅立叶变换离子回旋共振质谱仪对精氨酸-磷酸以及色氨酸-磷酸的非共价复合物离子进行了研究。结果显示,精氨酸和色氨酸均可与磷酸分子产生种类丰富、价态为+1和+2的复合物离子。而对不同体系的生成离子分布进行分析,则显示出不同体系间的差别。     

Characterisation of adducts of the lipid peroxidation product 4-hydroxy-2-nonenal and amyloid beta-peptides by liquid chromatography/electrospray ionisation mass spectrometry

Alzheimer's disease is characterised by brain neuritic plaques composed of a 39-44 amino acid peptide (Abeta). Lipid peroxidation is an early event induced by these amyloid beta-peptides, leading to the formation of 4-hydroxy-2-nonenal (HNE), which is one of the major end products of this process. HNE has been reported to form adducts via a stable covalent binding to proteins through a Michael addition to amino acid residues with a nucleophilic side chain. The present study reports an investigation of the conditions for formation of Abeta-HNE (Abeta 1-28 and Abeta 1-42) adducts, and their characterisation by liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI-MS). The results suggest that one or more HNE moieties are localised in the 6-16 region of these adducts, while Asp-1, Lys-16 and Lys-28 are not modified under the described reaction conditions.     

Analysis of cysteine-containing proteins using precolumn derivatization with <Emphasis Type="Italic">N</Emphasis>-(2-ferroceneethyl)maleimide and liquid chromatography/electrochemistry/mass spectrometry

N-(2-Ferroceneethyl)maleimide (FEM) is introduced as an electroactive derivatizing agent for thiol functionalities in proteins. Using appropriate reaction conditions, the derivatization is completed within five minutes and no unspecific labeling of free amino functions is observed. Liquid chromatography/electrochemistry/mass spectrometry was used to detect the reaction products. The reagent is a useful tool for determining the number of free thiol groups or the total number of free and disulfide-bound thiol groups in proteins. The electrochemical cell provides additional information, because the increase in mass spectrometric response upon electrochemical oxidation of the neutral ferrocene to the charged ferrocinium groups is monitored. The method was successfully applied to the analysis of native proteins and their tryptic digests. Dedicated to Prof. Werner Engewald on the occasion of his 70th birthday.     

Dual labeling of biomolecules using MeCAT and DOTA derivatives: application to quantitative proteomics

In this study, single and dual labeling of primary amino and thiol groups of target peptides is presented as a proof of concept. The proposed method allows flexible, independent and sequential labeling of the mentioned residues using lanthanides introduced via DOTA-complexes (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid). The efficiency of the method was optimized using cysteine-containing standard peptides and then applied to bovine serum albumin (BSA) and human serum albumin (HSA) to demonstrate qualitative and quantitative aspects of this strategy. For amino labeling, cysteinyl peptides were immobilized on Sepharose-6B resin and labeled with DOTA-NHS ester followed by metallation with lanthanides. Thiol labeling was carried out using lanthanide-containing metal-coded affinity tags (MeCAT) after elution of peptides from the resin. Complete dual labeling of the standard peptides was demonstrated by liquid chromatography electrospray ionization mass spectrometry, whereas more than 80% of the detected peptides of BSA and HSA were completely dual-labeled. Parallel detection by LC coupled to inductively coupled plasma mass spectrometry (ICP-MS) delivered reliable quantitative information. Thus, the versatile lanthanide choice in both labeling steps allowed estimating primary amino and thiol stoichiometries for the studied samples using different lanthanides. On the other hand, enhancement of ICP-MS signal was achieved as expected when all positions were labeled with the same lanthanide. Finally, linear calibrations of the signal for most of the labeled peptides by standard additions of digested BSA showed a suitable behaviour for quantitative applications and demonstrated the pre-concentration capability of the employed resin.     

Characterization of non-enzymatic acylation of amino or thiol groups of bionucleophiles by the acyl-adenylate or acyl-CoA thioester of cholic acid

Acyl-adenylates and acyl-CoA thioesters of bile acids (BAs) are highly electrophilic acyl-linked metabolites which can undergo transacylation reactions with amino and thiol groups of nucleophilic groups on acceptor molecules such as amino acids, peptides, and proteins. Here, non-enzymatic acylation at pH 7.4 of glycine, taurine, glutathione (GSH), and N-acetylcysteine (NAC) by cholyl-adenylate (CA-AMP) was compared with that mediated by cholyl-CoA thioester (CA-CoA) using a 1:1 mixture of stable isotopically labeled CA-AMP and unlabeled CA-CoA. The transacylation products of these substrates were analyzed by liquid chromatography/electrospray ionization linear ion-trap mass spectrometry in negative-ion detection mode. CA-AMP was more reactive than CA-CoA with the amino group of glycine or taurine than with the thiol group of GSH or NAC. In contrast, CA-CoA was more reactive than CA-AMP with the thiol group of GSH or NAC and was far less reactive with the amino group of glycine or taurine. These differences in the reactivity of CA-AMP as compared with that of CA-CoA towards amino and thiol groups may be attributed to the electrophilicity of the carbonyl carbon of these acyl-linked cholic acid metabolites and the nucleophilicity of the amino and thiol group in the bionucleophiles that were studied.     

Characterization of covalent addition products of chlorogenic acid quinone with amino acid derivatives in model systems and apple juice by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry

High-performance liquid chromatography (HPLC) coupled to electrospray ionization tandem mass spectrometry (ESI-MS(n)) was used to study the covalent interactions between chlorogenic acid (CQA) quinone and two amino acid derivatives, tert-butyloxycarbonyl-L-lysine and N-acetyl-L-cysteine. In a model system at pH 7.0, the formation of covalent addition products was demonstrated for both derivatives. The addition product of CQA dimer and tert-butyloxycarbonyl-L-lysine was characterized by LC/MS(n) as a benzacridine structure. For N-acetyl-L-cysteine, mono- and diaddition products at the thiol group with CQA quinone were found. In apple juice at pH 3.6, covalent interactions of CQA quinone were observed only with N-acetyl-L-cysteine. Taking together these results and those reported by other groups it can be concluded that covalent interactions of amino side chains with phenolic compounds could contribute to the reduction of the allergenic potential of certain food proteins.