Mass spectrometry of 2-substituted-1-keto-3-aryl-5H-imidazo-(1,5-a)-pyrroles derived from Schiff bases of N-terminal prolyl peptides

We have been able to extend the use of Schiff base derivatives in peptide sequencing to N-terminal prolyl peptides. Earlier studies from this laboratory revealed that certain aromatic Schiff bases of peptide esters gave electron-impact mass spectra with relatively intense molecular, sequence and internal fragment ions. We observed that the reaction of N-terminal prolyl peptide esters with 4-dimethylaminonaphthaldehyde, p-dimethylaminobenzaldehyde and 2-pyridinecarboxaldehyde gave cyclization products which were found to be 2-substituted-1-keto-3-aryl-5H-imidazo-[1,5-a]-pyrrole derivatives. The molecular ion and many of the expected cleavages were prominent in the mass spectra. Deuterium labeling at the α-carbon, amide nitrogen, or other exchangeable positions has been used in assigning the structure. It was also confirmed by the fragmentation pattern of the products derived by permethylation of the peptide derivative with tetramethylammonium hydroxide. Comparable cleavage patterns were seen among the N-terminal prolyl peptides examined. Proline amide gave the corresponding cyclized product. With the inclusion of N-terminal prolyl peptides in the list of peptides that we have examined, we may now prepare volatile derivatives of peptides containing any of the protein amino acids in two steps: esterification and treatment with the appropriate aromatic aldehyde.     

纳升电喷雾串联质谱"序列对接法"确定多肽的加钠位点

用QuattroM icro三级四极串联质谱分析常见的20种氨基酸的加钠效果。结果表明,绝大多数氨基酸与钠离子的非共价键结合力很弱甚至没有,但脯氨酸和苯丙氨酸很容易形成加钠离子峰。采用“序列对接法”测出重组人酸性纤维细胞生长因子(rh-a FGF)C-端肽段的全序列,并确定钠离子的加成位点为该肽段的第6位脯氨酸(6Pro)。通过酸化样品溶液获得无加钠、无序列间隙的该肽全序列,与加钠肽段的序列一致。     

Microwave-assisted reaction of peptide formation by amino acid with phosphate:Exploration of the most possible channels for the origin of life

The formation of peptides and then protein by small abiological molecules clusters such as amino acid is a key stage in the origin of life[1]. More and more ex- perimental results showed that phosphate plays an important role in the formation of biomolecules in prebiotic chemical evolution. The principal reservoirs of biochemical energy are phosphates (such as ATP). The peculiar role of phosphates in contemporary life might suggest its essential role in prebiotic energy conversion, syntheses …     

Identification of degradation products of aspartyl tripeptides by capillary electrophoresis-tandem mass spectrometry

Capillary electrophoresis-electrospray tandem mass spectrometry (CE-MS/MS) has been used to identify degradation products of the aspartyl tripeptides Phe-Asp-GlyNH(2) and Gly-Asp-PheNH(2) following incubation of the peptides in acidic and alkaline solution. At pH 2, the dominant decomposition products resulted from cleavage of the peptide backbone amide bonds to yield the respective dipeptides and amino acids. In addition, the cyclic aspartyl succinimide intermediate was identified by its [M+H](+) at m/z = 319 and the MS/MS spectrum exhibiting a simple fragmentation pattern with the [C(8)H(10)N](+)-ion as the principal daughter ion (a(1) of Phe-Asp-GlyNH(2)). Deamidation of the C-terminal amide as well as isomerization and enantiomerization of the Asp residue occurred upon incubation at pH 10. alpha-Asp and the isomeric beta-Asp and most of the diastereomeric forms (corresponding to D/L-Asp) could be separated by CE. All isomers could be identified based on their MS/MS spectra. Peptides with the amino acid sequence Phe-Asp-Gly containing the regular alpha-Asp bond displayed a highly intense b(2) fragment ion and a low abundant y(2) ion. In contrast, the y(2) and a(1) fragment were high abundant daughter ions in the mass spectra of beta-Asp peptides while the b(2) ion exhibited a lower abundance. Differences in the MS/MS spectra of the isomers of the peptides with the sequence Gly-Asp-Phe were obvious but less pronounced. In conclusion, CE-MS/MS proved to be a useful tool to study the decomposition and enantiomerization of peptides including the isomerization of Asp residues, due to the combination of efficient separation of isomers by CE and their identification by MS/MS.     

Peptide damage under Fenton conditions is sequence-dependent

Peptides with two or more acidic amino acids are damaged to a greater extent than other peptides under Fenton conditions as revealed by treating a 29791 membered one-bead-one-compound peptide library with FeCl(3), sodium ascorbate and hydrogen peroxide.     

Characterization of a peptide family from the skin secretion of the Middle East Tree Frog Hyla savignyi by composition‐based de novo sequencing

A new tryptophyllin‐like peptide family was found in the skin secretion of the tree frog Hyla savignyi. Peptides were characterized by database‐independent sequencing strategies and specific ion fragmentation features were investigated. Skin secretions from specimens of Hyla savignyi were collected by mild electrical stimulation. Peptides were separated by reversed‐phase nano‐high‐performance liquid chromatography (nanoHPLC) and mass spectra were acquired online by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR‐MS). Peptides were characterized by manual de novo sequencing and by composition‐based sequencing (CBS), appearing mostly as C‐terminal free acids and as their acid amide analogs. Amide peptides yielded lower intensities of y‐type ions after collision‐induced dissociation (CID) than their acid analogs. A mechanism of internal b‐ion formation (positive ion mode) and of CO₂ elimination (negative ion mode) is proposed. We also exemplified phenomena such as the proline effect and formation of non‐direct sequence ions after sequence rearrangements. The occurrence of rearrangement products, of internal ions and of the proline effect made the CID spectra highly complex. CBS analysis nevertheless resulted in successful and highly reliable sequence analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

超高效液相色谱-质谱联用法监测人心房钠尿肽的化学合成

多肽作为神经递质、激素、受体等参与和调节许多重要的生命过程。随着对多肽结构与功能认识的深入,化学合成多肽在生物医药、生命分析等领域显示了重要价值。人心房钠尿肽（ANP）是一种由28个氨基酸组成的多肽类激素,其含量和代谢异常与心血管疾病、癌症等密切相关。针对ANP重要的生理功能,该文开展了ANP化学合成及其过程的监测与优化,设计了集固相合成线性直链多肽和液相氧化成环为一体的策略。基于高效液相色谱的分离性能和多级质谱的结构鉴定能力,建立了超高效液相色谱-串联质谱（UHPLC-MS/MS）分析新方法,对固相合成产物进行了分离分析,并对液相氧化方法进行了筛选和优化,最终分离纯化得到了目标多肽,为人心房钠尿肽的高效化学合成及氧化成环反应提供借鉴。     

A tris (2-carboxyethyl) phosphine (TCEP) related cleavage on cysteine-containing proteins

Introduced in the late 1980s as a reducing reagent, Tris (2-carboxyethyl) phosphine (TCEP) has now become one of the most widely used protein reductants. To date, only a few studies on its side reactions have been published. We report the observation of a side reaction that cleaves protein backbones under mild conditions by fracturing the cysteine residues, thus generating heterogeneous peptides containing different moieties from the fractured cysteine. The peptide products were analyzed by high performance liquid chromatography and tandem mass spectrometry (LC/MS/MS). Peptides with a primary amine and a carboxylic acid as termini were observed, and others were found to contain amidated or formamidated carboxy termini, or formylated or glyoxylic amino termini. Formamidation of the carboxy terminus and the formation of glyoxylic amino terminus were unexpected reactions since both involve breaking of carbon—carbon bonds in cysteine.     

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．     

How much peptide sequence information is contained in ion trap tandem mass spectra?

Matching peptide tandem mass spectra to their cognate amino acid sequences in databases is a key step in proteomics. It is usually performed by assigning a score to a spectrum-sequence combination. De novo sequencing or partial de novo sequencing is useful for organisms without sequenced genome or for peptides with unexpected modifications. Here we use a very large, high accuracy proteomic dataset to investigate how much peptide sequence information is present in tandem mass spectra generated in a linear ion trap (LTQ). More than 400,000 identified tandem mass spectra from a single human cancer cell line project were assigned to 26,896 distinct peptide sequences. The average absolute fragment mass accuracy is 0.102 Da. There are on average about four complementary b- and y-ions; both series are equally represented but y ions are 2- to 3-fold more intense up to mass 1000. Half of all spectra contain uninterrupted b- or y-ion series of at least six amino acids and combining b- and y-ion information yields on average seven amino acid sequences. These sequences are almost always unique in the human proteome, even without using any precursor or peptide sequence tag information. Thus, optimal de novo sequencing algorithms should be able to obtain substantial sequence information in at least half of all cases.     

CE-MS Identification of Amino Acid Sequence Inversion as a New Degradation Pathway of an Aspartyl Model Tripeptide

CE-MS was employed to identify two unknown degradation products of the model tripeptide Phe-α-Asp-Gly heated at 80 °C in aqueous solution at pH 7.4. Both compounds displayed essentially identical mass spectra indicating the presence of peptide diastereomers. The [M + H]⁺-ion at m/z 338 suggested a tripeptide composed of the amino acids Phe, Gly and Asp. The fragmentation pattern indicated that Phe was not located at the N-terminus. Subsequently, the linear peptide α-Asp-Phe-Gly and the branched peptide Asp(Gly)-Phe were synthesized and analyzed by CE-MS. The mass spectrum of synthetic α-Asp-Phe-Gly was identical to that of the unknown compounds confirming the structure of the degradation products. Asp(Gly)-Phe displayed a complex fragmentation pattern. In conclusion, amino acid sequence inversion represents another degradation pathway of Phe-α-Asp-Gly at pH 7.4 besides known reactions including isomerization, enantiomerization, cyclization to diketopiperazine derivatives and backbone hydrolysis. The mechanism of the rearrangement of the amino acid sequence is proposed to proceed via an aza-bridged intermediate.

     

氨基酸结构描述子矢量VHSE及其在肽QSAR中的应用

从20种天然氨基酸的50个物化性质出发，按照疏水、立体和电性特征将其分类后分别进行主成分分析，并将产生的得分矢量即VHSE(principal component score vector of hydrophilicity,steric，and electronic properties)作为氨基酸结构描述子用于肽的定量构效关系研究。与已有方法相比，VHSE描述子具有物化意义明确、结果更易解释等特点。应用该描述子并结合逐步回归变量筛选和偏最小二乘建模方法，在对苦味二肽和血管舒缓激肽促进剂等体系的定量构效关系研究中，均取得了优于已有文献的结果。     

Modelling of prebiotic synthesis and selection of peptides under isothermal conditions and thermal cycling mode

The model peptide synthesis from mixtures of amino acids was carried out under the thermal cycling and isothermal modes. The compositions of the obtained mixtures of products and the primary amino acid sequence of the synthesized peptides were determined by Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry in combination with high-performance liquid chromatography with the application of de novo sequencing of the synthesized products. The processes of abiogenous synthesis of peptides were shown to occur under relatively mild temperature conditions and give a substantially less number of peptides as compared with the possible statistical set. The evolution of the system takes place in the process of the synthesis in solid phase with the disappearance of a series of the most unstable peptides. The selection process with the formation of complementary peptides takes place in peptide synthesis under the thermal cyclic mode.     

Substrate specificity and novel selective inhibitors of TNF-alpha converting enzyme (TACE) from two-dimensional substrate mapping

We report a systematic analysis of the P1' and P2' substrate specificity of TNF-alpha converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. Initial truncation studies, using the amino acid sequence around the cleavage site in precursor-TNF-alpha, showed that good turnover was obtained with the peptide DNP-LAQAVRSS-NH2. Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1'-P2'-SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1' in combination with 20 different amino acids at P2'. The peptides were pooled, treated with purified microsomal TACE, and the reaction mixtures were passed over a streptavidin affinity column to remove unreacted substrate and the N-terminal biotinylated product. C-terminal cleavage products not binding to streptavidin were subjected to liquid chromatography/mass spectrometry analysis where individual products were identified and semiquantitated. 25 of the substrates were resynthesized as discrete peptides and assayed with recombinant TACE. The experiments show that recombinant TACE prefers lipophilic amino acids at the P1' position, such as phenylglycine, homophenylalanine, leucine and valine. At the P2' position, TACE can accommodate basic amino acids, such as arginine and lysine, as well as certain non-basic amino acids such as citrulline, methionine sulfoxide and threonine. These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1', and threonine and nitro-arginine at P2'.     

Peptide sequencing through N-terminal phosphonylation and electrospray ionization mass spectrometry

Peptides were phosphonylated at their N-termini by reacting with ethoxyphenylphosphinate in the presence of triethylamine and tetrachloromethane under mild conditions. The phosphonylated peptides were analyzed by tandem electrospray ionization mass spectrometry. N-Terminal phosphonylation selectively increased the intensities of b(n)-type ions relative to other ion types. The resulting simplified mass spectra clearly show the sequential loss of amino acid residues from the C-termini of peptides, providing a convenient and rapid method for peptide sequencing.     

Microwave enhanced Akabori reaction for peptide analysis

The Akabori reaction, devised in 1952 for the identification of C-terminus amino acids, involves the heating of a linear peptide in the presence of anhydrous hydrazine in a sealed tube for several hours. We report here a modified Akabori reaction that rapidly identifies the C-terminus amino acid in a polypeptide including its amino acid sequence information at both the C-terminus and the N-terminus. This modified methodology demonstrates the fundamentals of microwave chemistry applied to bioanalytical problems. In this modified process, hydrazinolysis has been accelerated by the application of microwave irradiation. In our reaction, the linear peptide and hydrazine solution, contained in a loosely covered conical flask, was exposed to a few minutes of irradiation using an unmodified domestic microwave oven. While the classical Akabori reaction required several hours, the microwave assisted reaction takes just minutes. If dimethyl sulfoxide is added to dilute the reaction mixture, the process is retarded enough to allow aliquots of the reaction mixture to be drawn every few minutes over a period of about an hour in order to study the progress of hydrazinolysis. Reaction products were monitored by mass spectrometry-primarily FAB-MS. In addition to providing sequence information, the microwave enhanced Akabori reaction quickly detects the presence of arginine (Arg) by converting each Arg to ornithine (Orn). Furthermore, certain amino acids, containing beta-SH, CO2H, and CONH2 groups in their side chain, are susceptible to modification by hydrazine, thereby, providing rapid confirmation of the presence of these amino acid residues. In these preliminary studies, the following oligopeptides were analyzed to demonstrate the effectiveness of our approach; the dipeptide (Trp-Phe), the tripeptide (Tyr-Gly-Gly), the tetrapeptide (Pro-Phe-Gly-Lys), the heptapeptide (Ala-Pro-Arg-Leu-Arg-Phe-Tyr), and a N-terminal blocked tripeptide (N-acetyl-Met-Leu-Phe).     

Characterisation of interferon α‐2b by liquid chromatography and mass spectrometry techniques

Interferon α‐2b produced by Escherichia coli consists of 165 amino acids and contains two disulphide bonds; its purity was confirmed by LC‐UV (DAD)‐FLD and LC‐MS techniques. A C₄ column was used with UV detection at 214 nm; diode array detector (DAD) spectra were recorded from 200–400 nm and fluorescence detection was performed at specific wavelengths of trypthophan emission and excitation. Peptide mapping was performed with trypsin. Peptides produced by trypsin digestion were analysed by LC‐UV (DAD)‐FLD, LC‐MS, and LC‐MS/MS using a C₁₈ column. Amino acid sequence coverage was about 95%. UV spectra in the range from 200 nm to 400 nm, emission (Em) and excitation (Ex) spectra of each separated peptide were additionally compared with spectra of the same peptide produced by digestion of European Pharmacopaeia interferon α‐2b standard (spectral matching). The chromatogram of any interferon α‐2b (drug substance or certificated standard) sample produced in the same manner with the same amino acid composition should be similar to the chromatogram obtained by the method described in this paper. Molecular masses of peptides were obtained from MS experiments and MS/MS experiments gave additional structural information. The molecular mass of interferon α‐2b was obtained by MALDI‐TOF MS analysis in linear mode, with an accuracy comparable to the theoretical average mass ± 5 atomic mass units. The molecular mass was obtained from the deconvoluted ESI mass spectrum.     

Modeling peptide mass fingerprinting data using the atomic composition of peptides

The peptide mass fingerprinting technique is commonly used for identifying proteins analyzed by mass spectrometry (MS) after enzymatic digestion. Our goal is to build a theoretical model that predicts the mass spectra of such digestion products in order to improve the identification and characterization of proteins using this technique. We present here the first step towards a full MS model. We have modeled MS spectra using the atomic composition of peptides and evaluated the influence that this composition may have on the MS signals. Peptides deduced from the SWISS-PROT protein sequence database were used for the calculation. To validate the model, the variability of the peptide mass distribution in SWISS-PROT was compared to two theoretical, randomly generated databases. Functions have been built that describe the behavior of the isotopic distribution according to the mass of peptides. The variability of these functions was analyzed. In particular, the influence of sulfur was studied. This work, while representing only a first step in the construction of an MS model, yields immediate practical results, as the new isotopic distribution model significantly improves peak detection in MS spectra used by protein identification algorithms.     

Identification of leucine-enkephalin radical oxidation products by liquid chromatography tandem mass spectrometry

The oxidation of the peptide leucine-enkephalin (YGGFL) induced by the hydroxyl radical (HO*), formed under Fenton-like conditions [Cu (II)/H(2)O(2)], was studied and monitored by LC-MS. The oxidation products identified included products resultant from (a) the insertion of oxygen atoms (1-5), (b) peptide backbone cleavage (short-chain products formed by diamide pathway) and (c) radical-radical crosslinking reactions. In order to identify the modified residues, LC-MS/MS spectra were obtained. The insertion of oxygen atoms into the peptide originated hydroxide, di-hydroxide and/or hydroperoxide derivatives. In addition it was found that the aromatic amino acids are most susceptible to being hydroxylated, while the aliphatic amino acids are more prone to forming hydroperoxides. Oxidation products with double bonds were also identified. The short chain products resulted from the alpha-carbon radical of terminal amino acids (Tyr and Leu). Products resulting from cross-linking reactions between intact carbon-centered peptide radical (with and without one HO group) and a side chain radical (*C(7)H(7)O) were identified. It was found that, although all amino acids residues of the peptide undergo modifications, the N-terminal seems to be prone to oxidative modifications under these conditions.     

Formation of diagnostic product ions from cyanobacterial cyclic peptides by the two-bond fission mechanism using ion trap liquid chromatography/multi-stage mass spectrometry

Product ions obtained by tandem mass spectrometry (MS/MS) are quite effective for the amino acid sequencing of linear peptides. However, in the case of cyclic peptides, the fragmentation pattern is complicated because the cleavages occur randomly and product ions are generated as a(n), b(n), c(n), x(n), y(n) and z(n) series ions; therefore, the authors have never obtained sufficient sequence information. In order to overcome this problem, we applied ion trap liquid chromatography/multi-stage mass spectrometry (LC/MS(n)) and characterized the product ions obtained from anabaenopeptins and aeruginopeptins as the cyclic peptides. For the anabaenopeptins, MS(2) analysis did not provide sufficient sequence information on the cyclic structure, and MS(3) analysis was applied to sequence the constituent amino acids. Diagnostic product ions were obtained by the MS(3) analysis and were quite effective for obtaining the sequence information of the constituent amino acids. MS(2) analysis was, however, sufficient to obtain the sequence information of the aeruginopeptins. In both cases, the resulting product ions obtained from the cyclic structures were formed by the two-bond fission mechanism of the precursor ion, in which an initial fission of the cyclic structure to a linear one and subsequent fission(s) at the peptide bonds are included. The fragmentations were similar for the structurally related compounds, indicating that the cleavages occurred at definite peptide bonds. In addition, the resulting product ions are generated as b(n) series ions and the mass difference facilitates the amino acid sequencing. Thus, ion trap LC/MS(n) provides sequence information, and the resulting product ions are reproducible among the structurally related compounds and reliable for the sequencing of the constituent amino acids of the cyclic structure.