A novel class of chemically modified iodo-containing resins: design, synthesis and application to mass spectrometry-based proteome analysis

A novel class of chemically modified iodo-containing resins with isotope-labeled tagging for mass spectrometry-based proteome analysis is described. This iodo-containing resin contains a thiol-reactive group that is used to capture the cysteine (Cys)-containing peptides from peptide mixtures, one 'tag' amino acid, and an aminomethyl polystyrene resin with Rink Amide Linker. The 'tag' amino acid is synthesized in both heavy and light isotope-coded forms and therefore permits the direct relative quantification of peptides/proteins through mass spectrometric analysis. In the iodo-containing resin strategy, the Cys-containing peptides of two samples covalently captured by either light or heavy iodo-containing resin were mixed and washed extensively under stringent conditions. Then the Cys-containing peptides were retrieved by acid-catalyzed elution. Finally, the eluted peptides were directly analyzed by micro liquid chromatography/mass spectrometry for identification and relative quantification. The iodo-containing resins were synthesized by a simple but effective method. Their abilities to identify and quantify the Cys-containing part in two samples were proved by the analysis of mixtures of amino acids, peptides and proteins.     

反应时间、温度和溶剂对缬氨酸自组装成聚合肽反应的影响

寡肽类化合物一般具有较强的生物活性,多数可作为药物或药物前体,因此成为人们的研究热点之一．目前寡肽的合成方法主要有液相法、固相法及酶促合成法,这些合成方法往往需要对氨基酸的活性基团进行选择性保护,步骤繁琐．近期研究发现,在水-醇体系中α-氨基酸被磷酰化为N-磷酰-α-氨基酸后,可发生自组装聚合肽反应;在无水条件下,N,O-二(三甲基硅基)-α-氨基酸可与磷酰化试剂如O,O-亚苯基磷酰氯反应生成N-磷酰-α-氨基酸,后者也可通过自组装反应得到二～八肽,但这些N-磷酰-α-氨基酸的制备均需使用有机磷试剂．我们发现,在无机磷试剂如PCl5等辅助下,α-氨基酸同样可以发生自组装反应,得到一系列寡聚肽,这既可为寡聚肽的合成提供一种新的方法,同时,因无机磷试剂在原始地球条件下更可能存在,因而对于揭示多肽及蛋白质的起源具有重要意义．氨基酸的自组装反应具有链锁反应的特点,因此必须控制反应条件实现对反应的控制。     

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 Novel Approach to Reversed-Phase Preparative High-Performance Liquid Chromatography of Peptides

Abstract

In this study, we describe a novel approach to preparative liquid chromatography which takes advantage of the different relative hydrophobicities of components of a sample mixture, so that when a column is optimally loaded with an aqueous solution of the sample mixture, there is competition among the sample components for the adsorption sites on the hydrophobic stationary phase. The more hydrophobic components compete more successfully for these sites than more hydrophilic components, which are displaced and immediately eluted from the column. Thus, the major separation takes place in water. Subsequent treatment with an aqueous organic modifier is only required to wash retained components off the column and takes no part in the major separation process. This approach was applied to the preparative purification of mixtures of closely-related peptides, representing the crude peptide mixtures typically obtained from solid-phase peptide synthesis. The excellent separation profiles and high yields of pure peptide products on analytical columns reported in this study demonstrate that this methodology has great potential for preparative separation of a major component from hydrophilic and/or hydrophobic impurities.     

Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions

Formaldehyde cross-linking of proteins is emerging as a novel approach to study protein-protein interactions in living cells. It has been shown to be compatible with standard techniques used in functional proteomics such as affinity-based protein enrichment, enzymatic digestion, and mass spectrometric protein identification. So far, the lack of knowledge on formaldehyde-induced protein modifications and suitable mass spectrometric methods for their targeted detection has impeded the identification of the different types of cross-linked peptides in these samples. In particular, it has remained unclear whether in vitro studies that identified a multitude of amino acid residues reacting with formaldehyde over the course of several days are suitable substitutes for the much shorter reaction times of 10-20 min used in cross-linking experiments in living cells. The current study on model peptides identifies amino-termini as well as lysine, tryptophan, and cysteine side chains, i.e. a small subset of those modified after several days, as the major reactive sites under such conditions, and suggests relative position in the peptide sequence as well as sequence microenvironment to be important factors that govern reactivity. Using MALDI-MS, mass increases of 12 Da on amino groups and 30 Da on cysteines were detected as the major reaction products, while peptide fragment ion analysis by tandem mass spectrometry was used to localize the actual modification sites on a peptide. Non-specific cross-linking was absent, and could only be detected with low yield at elevated peptide concentrations. The detailed knowledge on the constraints and products of the formaldehyde reaction with peptides after short incubation times presented in this study is expected to facilitate the targeted mass spectrometric analysis of proteins after in vivo formaldehyde cross-linking.     

Easy Production of “Difficult Peptides” Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site

Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.     

Electrospray ionization mass spectrometric analysis of complexes between peptide‐derived Amadori products and borate ions

Hexose‐modified peptides, products of the enzymatic hydrolysis of glycated proteins, could be used as markers of diabetes mellitus, the aging process and other diseases. The main difficulty in this approach is the detection of glycated peptides in the complex mixtures of compounds. In this study we investigated the formation of borate complexes of the peptide‐derived Amadori products by high‐resolution mass spectrometry (HRMS) and tandem mass spectrometry (MS/MS) experiments. It was found that the formation of a complex with the borate ion stabilizes the sugar moiety, resulting in the simplification of the fragmentation patterns of peptide‐derived Amadori products. The level of dehydration, as well as the elimination of formaldehyde from the precursor ions of borate complexes, was lower as compared to the free peptide. On the other hand the intensity of the b‐ and y‐type ions for borate complexes is significantly higher in comparison to the free peptide‐derived Amadori product. Moreover, the elimination of a whole hexose moiety was not detected in the examined peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

低浓度甲醛对多肽和蛋白化学修饰的质谱研究

采用基质辅助激光解析电离飞行时间质谱( MALDI-TOF MS)和纳升电喷雾四极杆飞行时间串联质谱( Nano-ESI -QTOF MS)技术,以标准肽段和流感病毒基质蛋白酶切肽段为模型,研究了甲醛对蛋白质和多肽主链的修饰作用。采用与实际病毒灭活过程一致的实验条件(4℃,0.025%(V/V)福尔马林(37%(w/w)甲醛溶液)处理72 h),进行甲醛与多肽的化学反应。结果表明,在实验条件下,甲醛能与标准肽段N端的氨基反应生成羟甲基加合物,再发生缩合反应生成亚胺,形成+12 Da的产物。此外,甲醛还能与标准肽段中的精氨酸、赖氨酸的侧链发生反应,生成+12 Da的反应产物。对流感病毒基质蛋白的酶切肽段与甲醛的反应的质谱分析结果显示,多数的肽段都生成了+24 Da的产物,质量的增加来源于肽段N端氨基(+12 Da)和C端精氨酸或赖氨酸的侧链(+12 Da)的贡献。此外,还观察到有一个漏切位点的肽段生成了+36 Da的产物。本研究结果表明,在实验条件下,低浓度甲醛主要与肽段和蛋白的N 端氨基,以及精氨酸和赖氨酸侧链发生反应。本研究为分析低浓度甲醛与蛋白质的反应产物提供了有效的质谱分析方法和解谱依据。     

Nitrite anions induce nitrosative deamination of peptides and proteins

In the present study, reactions of sodium nitrite with proteins/peptides were characterized with mass spectrometry. The reaction generates two major products: replacement of the amino group by a hydroxyl group and formation of an alkene derivative by loss of a NH3 group at the N-terminus and the side chain of lysine residues of proteins/peptides. The reaction proceeds rapidly in weak acidic solution and at 37 degrees C in the presence of a millimolar concentration of nitrite, demonstrating that nitrite induces nitrosative deamination in proteins and peptides. The facile nitrite-induced modification of amino groups of protein/peptides changes the chemical nature of proteins and may have various applications in peptide synthesis, analytical chemistry, and protein engineering. It also provides information to enhance our understanding of functions of nitrite ions in biology and food preservation.     

Intermolecular condensation products formed during the pyrolysis of peptides

Mass Spectrometry (MS) analysis of pyrolysis products of simple peptides has revealed several non-volatile thermal degradation products at masses lower than the precursor peptide. In addition to these products, many other signals were also observed at higher masses than the precursor peptide, and their characterization is the focus of this study. Here we report on the observation of homo and hetero condensation peptide products formed during the pyrolysis of peptides. The observed peptide condensation products are formed between two, three or even four peptides. Tandem MS (MS/MS) analyses of these products showed that C-terminal to N-terminal intermolecular bonding is preferred during pyrolysis when combining two peptides, rather than involving crosslinking between basic and acidic side chain groups like arginine and aspartic acid. These observations are rationalized by steric hindrance effect and known pK_a values of the peptide C- and N-termini and amino acid side groups like aspartic acid and arginine. Pyrolysis of a standard N-acetylated peptide showed no detectable condensation and/or crosslinked products, even in peptides with basic side groups, providing further evidence for the C-terminus to N-terminus intermolecular bonding between peptides under pyrolytic conditions.     

Thermal degradation of deoxybenzoin polymers studied by pyrolysis-gas chromatography/mass spectrometry

The thermal degradation behavior of novel ultra-fire-resistant polymers and copolymers containing deoxybenzoin units in the backbone was studied by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). The polymers were synthesized by the polycondensation of 4,4′-bishydroxydeoxybenzoin (BHDB) with isophthaloyl chloride (to give polyarylates), phenylphosphonic dichloride (to give polyphosphonates), and their mixtures (to give poly(arylate-co-phosphonate) copolymers). The thermal decomposition, under nitrogen conditions, of BHDB-polyarylate was characterized by a simultaneous degradation of both the bisphenolic (deoxybenzoin) and isophthalate sub-units, whereas a three-step decomposition phenomenon was observed for the BHDB-polyphosphonate. BHDB-polymers containing phosphonate groups in the backbone did not show any phosphorus-based volatile decomposition products, whereas the corresponding bisphenol A-based polyphosphonates released volatile decomposition products comprised mainly of phosphorus-containing compounds.     

Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability

Recently various methods for the N-terminal sulfonation of peptides have been developed for the mass spectrometric analyses of proteomic samples to facilitate de novo sequencing of the peptides produced. This paper describes the isotope-coded N-terminal sulfonation (ICenS) of peptides; this procedure allows both de novo peptide sequencing and quantitative proteomics to be studied simultaneously. As N-terminal sulfonation reagents, 13C-labeled 4-sulfophenyl[13C6]isothiocyanate (13C-SPITC) and unlabeled 4-sulfophenyl isothiocyanate (12C-SPITC) were synthesized. The experimental and reference peptide mixtures were derivatized independently using 13C-SPITC and 12C-SPITC and then combined to generate an isotopically labeled peptide mixture in which each isotopic pair differs in mass by 6 Da. Capillary reverse-phase liquid chromatography/tandem mass spectrometry experiments on the resulting peptide mixtures revealed several immediate advantages of ICenS in addition to the de novo sequencing capability of N-terminal sulfonation, namely, differentiation between N-terminal sulfonated peptides and unmodified peptides in mass spectra, differentiation between N- and C-terminal fragments in tandem mass spectra of multiply protonated peptides by comparing fragmentations of the isotopic pairs, and relative peptide quantification between proteome samples. We demonstrate that the combination of N-terminal sulfonation and isotope coding in the mass spectrometric analysis of proteomic samples is a viable method that overcomes many problems associated with current N-terminal sulfonation methods.     

The contributions of specific amino acid side chains to signal intensities of peptides in matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of complex peptide mixtures is often hampered by signal suppression effects as well as certain intrinsic properties of specific peptides that influence the desorption/ionization behavior. The present systematic study reports on the relationship between the occurrence of certain amino acids in peptides and the intensities of the related ions which appear during MALDI-MS analysis for both tryptic digests of proteins and synthetic peptide mixtures. The analysis of the tryptic digests revealed that the peptide sequences of the most intense peaks detected by MALDI-MS contained significantly higher proportions of arginine, phenylalanine, proline, and leucine than the average values for the measured proteins. The relationship between the relative signal intensities and amino acid compositions of peptides was studied in more detail by the partial least squares (PLS) method using equimolar mixtures of 144 well-characterized synthetic peptides. The regression coefficients clearly indicated that the presence of arginine, phenylalanine, leucine and proline tend to enhance the desorption/ionization process which results in higher MALDI-MS peak intensities. Furthermore, it was shown that the impact of arginine depends strongly on the identity of adjacent amino acids.     

Separation and characterization of complex crude mixtures produced in the synthesis of therapeutic peptide hormones by liquid chromatography coupled to electrospray mass spectrometry (LC-ES-MS)

Native peptides and peptidomimetics can be synthesized in a routine way by rapid and efficient procedures. However, the final products always result in complex mixtures, in which the target peptide is contaminated with undesired side products and other impurities. Thus, it is imperative to develop analytical methods for the evaluation of the target peptide’s purity in order to obtain an effective, safe and legal pharmaceutical product. LC-ES-MS is used here in order to separate and characterize the side-products associated with several synthetic hormones with therapeutic interest: carbetocin, eledoisin, leuprolide, goserelin and triptorelin. General directions for LC-ES-MS analysis of the synthetic peptide mixtures are established. Mass information obtained offers a significant advantage for the purity assessment of therapeutic hormones and gives a key tool to enhance their process of synthesis.     

微波促进催产素和赖氨加压素环肽的固相合成

以Rink Amide-MBHA树脂为载体, 采用Fmoc/tBu正交保护固相合成策略, 运用微波照射促进, 先快速高效地合成得到载有催产素或赖氨加压素还原型多肽的树脂, 再将连接在树脂上的各还原型多肽分别在微波促进条件下和常温条件下环合形成二硫键制得环肽, 最后用Reagent K试剂将环肽从树脂上裂解下来得到目标多肽的粗品. 利用HPLC法测定不同固相环合条件下得到的多肽粗品纯度, 结果显示经微波促进固相环合得到的多肽粗品纯度明显高于常温条件下得到的多肽粗品纯度. 粗品最后经过反相制备高效液相系统纯化并冻干得到目标多肽纯品, 通过电喷雾质谱法测定了制得的还原型多肽及相应环肽的分子量, 验证了它们的结构.     

The relative influence of phosphorylation and methylation on responsiveness of peptides to MALDI and ESI mass spectrometry

Qualitative and quantitative analysis of post‐translational protein modifications by mass spectrometry is often hampered by changes in the ionization/detection efficiencies caused by amino acid modifications. This paper reports a comprehensive study of the influence of phosphorylation and methylation on the responsiveness of peptides to matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. Using well‐characterized synthetic peptide mixtures consisting of modified peptides and their unmodified analogs, relative ionization/detection efficiencies of phosphorylated, monomethylated, and dimethylated peptides were determined. Our results clearly confirm that the ion yields are generally lower and the signal intensities are reduced with phosphopeptides than with their nonphosphorylated analogs and that this has to be taken into account in MALDI and ESI mass spectrometry. However, the average reduction of ion yield caused by phosphorylation is more pronounced with MALDI than with ESI. The unpredictable impact of phosphorylation does not depend on the hydrophobicity and net charge of the peptide, indicating that reliable quantification of phosphorylation by mass spectrometry requires the use of internal standards. In contrast to phosphorylation, mono‐ and dimethylated peptides frequently exhibit increased signal intensities in MALDI mass spectrometry (MALDI‐MS). Despite minor matrix‐dependent variability, MALDI methods are well suited for the sensitive detection of dimethylated arginine and lysine peptides. Mono‐ and dimethylation of the arginine guanidino group did not significantly influence the ionization efficiency of peptides in ESI‐MS. Copyright © 2009 John Wiley & Sons, Ltd.     

Hot or not—the influence of elevated temperature and microwave irradiation on the solid phase synthesis of an affibody

Despite the advances of solid phase peptide synthesis (SPPS) the synthesis of long peptides is still challenging. Microwave irradiation and conventional heating are considered to improve the efficiency of SPPS. It has been shown that conventional heating and heating by microwave irradiation improves the efficiency of solid phase synthesis of peptides that are prone to aggregation as compared to the synthesis at room temperature. In this Letter, the influence of elevated temperature and microwave irradiation on the homogeneity of the synthesis product of a 58-mer peptide affibody has been compared. A detailed analysis by high resolution HPLC and LC-MS mass spectrometry using a high-mass resolution Orbitrap Exactive mass spectrometer was performed. This study revealed that neither thermal heating nor microwave heating improves the yield and purity of the crude product as compared to the synthesis at room temperature. In contrast, the formation of undesirable side products rather increased by microwave irradiation. These results indicate that neither heating nor microwave enhancement of solid phase synthesis does allow a significant improvement of peptide sequences with a low aggregation potential.     

Design of a sheathless capillary eletrophoresis-mass spectrometry probe for operation with a Z-spray ionization source

The construction of a sheathless interface for capillary electrophoresis-electrospray ionization mass spectrometry (CE-ESI-MS), for operation with a Z-Spray source on a Micromass Quattro-LC triple quadrupole mass spectrometer is described. Designing the interface involved machining a probe compatible with the setup already in place on the mass spectrometer, i.e., MegaFlow-Z ESI. The probe was made of Lexan with the same dimensions as the ESI probe supplied with the instrument. The electrical connection at the electrospray end of the CE capillary was made possible by gold-coating (sheathless CE-ESI-MS). The probe design as well as the electrical and power supply requirements are described in detail. Experiments were performed using this interface, and CE separations of mixtures containing pmole and sub-pmole amounts of peptides were monitored by on-line MS. For a standard peptide mixture (10(-4) M), separation efficiency was typically characterized by N > 10(4) theoretical plates with S/N > 400. Using the same experimental setup, it was also possible to conduct on-line CE-ESI-tandem MS (MS/MS) experiments on the same peptide mixture, and to determine the sequence of the peptides. MS/MS scan functions for different precursor ions were used either alternately or sequentially and the results from both methods were compared. The possibility of peptide mass mapping was explored, and CE-ESI-MS results were obtained for the digestion products of equine myoglobin. Separation efficiencies and S/N values were similar to those obtained for standard peptides. A complete map of the digestion products was obtained.     

Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.

We have demonstrated the use of per-methyl esterification of peptides for relative quantification of proteins between two mixtures of proteins and automated de novo sequence derivation on the same dataset. Protein mixtures for comparison were digested to peptides and resultant peptides methylated using either d0- or d3-methanol. Methyl esterification of peptides converted carboxylic acids, such as are present on the side chains of aspartic and glutamic acid as well as the carboxyl terminus, to their corresponding methyl esters. The separate d0- and d3-methylated peptide mixtures were combined and the mixture subjected to microcapillary high performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Parent proteins of methylated peptides were identified by correlative database searching of peptide tandem mass spectra. Ratios of proteins in the two original mixtures could be calculated by normalization of the area under the curve for identical charge states of d0- to d3-methylated peptides. An algorithm was developed that derived, without intervention, peptide sequence de novo by comparison of tandem mass spectra of d0- and d3-peptide methyl esters.     

Electron capture dissociation of singly and multiply phosphorylated peptides

Analysis of phosphotyrosine and phosphoserine containing peptides by nano-electrospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry established electron capture dissociation (ECD) as a viable method for phosphopeptide sequencing. In general, ECD spectra of synthetic and native phosphopeptides appeared less complex than conventional collision activated dissociation (CAD) mass spectra of these species. ECD of multiply protonated phosphopeptide ions generated mainly c- and z(.)-type peptide fragment ion series. No loss of water, phosphate groups or phosphoric acid from intact phosphopeptide ions nor from the c and z(.) fragment ion products was observed in the ECD spectra. ECD enabled complete or near-complete amino acid sequencing of phosphopeptides for the assignment of up to four phosphorylation sites in peptides in the mass range 1400 to 3500 Da. Nano-scale Fe(III)-affinity chromatography combined with nano-electrospray FTMS/ECD facilitated phosphopeptide analysis and amino acid sequencing from crude proteolytic peptide mixtures.