氨基酸组成相同序列不同的小分子多肽的液相色谱-质谱联用分析

多肽组学是近年来兴起的一门新型学科,质谱已成为多肽组学研究的强有力手段．然而,用于检测具有相同氨基酸组成但序列不同的多肽时,只能给出等同的分子离子峰,在多肽结构解析上受到一定限制．因此,发展色谱分离．质谱检测联用技术是分析具有相同氨基酸组成但序列不同的多肽的有效途径．本文建立了一种氨基酸组成相同序列不同的小分子多肽的反相液相色谱分离-电喷雾离子化质谱检测新方法．该方法采用高效液相色谱-质谱联用技术,以两种三肽Gly．Ser．Phe和Gly．Phe．Ser为模式样品对象,考察了小分子多肽在不同流动相组成、流动相添加剂及pH等条件下的液相色谱行为,并讨论其保留机理．研究结果表明,在最优化的实验条件下,该方法稳定性好,重现性高,为多肽组学研究中的多肽解析提供科学的分析方法．     

Applicability of the critical chromatography concept to proteomics problems: Dependence of retention time on the sequence of amino acids

A peptide separation model based on the technique of liquid chromatography of macromolecules at the critical condition was proposed. In terms of this model, the array of experimental data on the separation of peptides is considered. The main phenomenological parameters of the model—effective adsorption energies of amino acid residues—were determined, thus allowing the influence of character of their alternation in the chain on retention times to be predicted. The model is applicable to investigation into the feasibility of separation in different chromatographic modes of not only peptides with the same amino acid composition and different sequences of units in the chain but also peptides containing amino acid isomers and mirror sequences with different terminal groups.     

A database of 660 peptide ion cross sections: Use of intrinsic size parameters for bona fide predictions of cross sections

An ion trap/ion mobility/time-of-flight mass spectrometry technique has been used to measure collision cross sections for 660 peptide ions generated by tryptic digestion of 34 common proteins. Measured cross sections have been compiled into a database that contains peptide molecular weight and sequence information. The database is used to generate average intrinsic contributions to cross section (size parameters) for different amino acid residues by solving systems of equations that relate the unknown contributions of individual residues to the sequences and cross sections of database peptides. Size parameters are combined with information about amino acid composition to calculate cross sections for database peptides. Bona fide cross section predictions (made prior to measurement) for peptides observed in tryptic digests of sperm whale myoglobin and yeast enolase are made. Eight of 10 predicted cross sections are within 2% of the experimental values and all 10 are within 3.2%. The utility of size parameters for cross section prediction is explored and discussed.     

HPLC Off-Line Mass Spectrometry MALDI of Amino Acids in Carbon Sorbents

A high performance liquid chromatography and a mass spectrometry matrix-assisted laser desorption/ionization (MALDI) methods were used to select the conditions of both successful separation and to identify amino acids and peptides on the carbon sorbents. For the first time the graphitized and nongraphitized carbon blacks were used for the identification of amino acids and peptides by the MALDI method. It was shown that an increased surface area of carbon blacks led to a sharp increase in the intensities of the detected peaks of protonated molecular ions and adducts with alkali metal cations of the amino acids and peptides under study.     

栝楼蛋白 2: 栝楼蛋白部分化学结构的初步测定

栝楼蛋白(Trichobitacin)是从栝楼(Trichosanthes kirilowiiMaxim, Cucurbitaceae)中新发现的核糖体失活蛋白, 分子量为27,228; pI为9.6。应用基质辅助的激光解析飞行时间质谱(MALDI-TOF-MS)和快原子轰击质谱法(FAB-MS)分别测定胰蛋白酶酶解栝楼蛋白和天花粉蛋白(Trichosanthin)的混合肽质谱, 通过比较发现了一些分子量相同的肽。由于这两种蛋白质都来源于栝楼块根, 同源性比较强, 所以这些肽序列在两种蛋白质中基本一样; 再结合蛋白N-端自动顺序仪测定栝楼蛋白N-端的结果, 确定了栝楼蛋白N-端38个氨基酸的顺序, 栝楼蛋白经胰蛋白酶酶解后所得肽段用HPLC分离纯化, 再用蛋白质自动顺序仪, DABITC/PITC双偶合手工法和质谱法共确定了栝楼蛋白N-端, C-端等100多个氨基酸残基的序列。     

Edman降解中异硫氰酸苯酯新修饰位点的发现和验证

Edman降解是最早建立的一种用于多肽和蛋白质氨基端测序的方法,该方法现在仍被广泛用于生物化学领域。随着高通量蛋白质组学技术的发展和应用,该方法中的异硫氰酸苯酯反应被用于修饰蛋白质氨基端,并用于检测蛋白质水解位点。但还没有异硫氰酸苯酯是否可以修饰其他氨基酸侧链并影响多肽序列分析的研究。为了探究其修饰其他氨基酸的可能性,本文利用基质辅助激光解吸电离飞行时间质谱（MALDI-TOF-MS）和液相色谱-串联质谱（LC-MS/MS）研究了异硫氰酸苯酯对一个模型肽的化学修饰。质谱数据解析后发现在高浓度异硫氰酸苯酯的反应条件下,组氨酸上可以引入一个新的异硫氰酸苯酯修饰位点。这一修饰位点的发现预示着通过改变实验条件或分析方法,可以更准确地利用Edman降解和蛋白质组学技术分析多肽和蛋白质。     

基于深度学习的保留时间预测方法的研究进展及应用

在基于液相色谱-质谱联用的蛋白质组学研究中,肽段的保留时间作为有效区分不同肽段的特征参数,可以根据肽段自身的序列等信息对其进行预测.使用预测得到的保留时间辅助质谱数据鉴定肽段序列可以提高鉴定的准确性,因此对保留时间预测的工作一直受到领域内的广泛关注.传统的保留时间预测方法通常是根据氨基酸序列计算肽段的理化性质,进而计算...     

Open-tubular capillary electrochromatography-mass spectrometry with sheathless nanoflow electrospray ionization for analysis of amino acids and peptides

A novel, rugged sheathless capillary electrochromatography-electrospray ionization (CEC-ESI) device, in which an open-tubular separation capillary and an electrospray tip are integrated with a Nafion tubing junction, is coupled to mass spectrometry (MS) for the analysis of amino acids and peptides. A stable electrospray was generated at nanoflow rates by applying a positive electrical potential at the Nafion membrane junction. To sustain the stable spray, an electroosmotic flow (EOF) to the spray was supported by coating the fused silica capillary with Lupamin, a high-molecular-weight linear positively charged polyvinylamine (PVAm) polymer, which also minimizes analyte adsorption. Electrochromatographic separation of amino acids and peptides was further enhanced by the chromatographic selectivity of Lupamin stationary phase for these molecules. The device was very reliable and reproducible for CEC-ESI-MS analyses of amino acids and peptides for over a hundred injections. The separation and detection behaviors of amino acids and peptides under different conditions including pH, concentration, and composition of mobile phases on Lupamin-coated and uncoated capillaries have been investigated. The relationship between nano electrospray stability and EOF is discussed.     

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.     

Open-tubular electrochromatographic characterization of synthetic peptides

The open-tubular electrochromatographic (OT-CEC) migration behavior of a series of peptides, based on a common structural feature, has been characterized using two different types of chemically modified etched capillaries. The organic moieties immobilized onto the capillary inner surface were n-butylphenyl and cholesterol-10-undecenaoate, respectively. The structure-migration behavior of this set of peptides has been studied at several pH values and with methanol at different concentrations as an organic solvent modifier of the buffer electrolyte composition. By comparing the structural properties of the peptides, such as their amino acid sequences, charge-to-mass ratios and intrinsic hydrophobicities to their migrational behavior, the relative contribution of electrophoretic and chromatographic mobility to the overall migration times, elution order, and selectivity has been determined. Moreover, the experimental data provide important insight into procedures that can be used to modulate the separation of peptides in OT-CEC through variation of the composition of the electrolyte buffer as well as via the properties of the bonded organic moiety.     

An integrated serum proteomic approach capable of monitoring the low molecular weight proteome with sequencing of intermediate to large peptides

The low‐abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low‐abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time‐of‐flight MS instrument. As a demonstration of the approach, two low‐abundance peptides with masses of ～4000–5000 Da were selected for MS/MS sequencing. The multi‐channel analyzer (MCA) was used in a novel way that allowed for summation of 120 fragmentation spectra for each of several customized collision energies, providing more thorough fragmentation coverage of each peptide with improved signal to noise. The peak list from this composite analysis was submitted to Mascot for identification. The two index peptides, 4279 Da and 5061 Da, were successfully identified. The peptides were a 39 amino acid immunoglobulin G heavy chain variable region fragment and a 47 amino acid fibrin alpha isoform C‐terminal fragment. The method described here provides the ability both to survey thousands of serum molecules and to couple that with markedly enhanced cLC/MS/MS peptide sequencing capabilities, providing a promising technique for serum biomarker discovery. Copyright © 2009 John Wiley & Sons, Ltd.     

Interactions and uses of antisense peptides in affinity technology.

Antisense peptides, amino acid sequences encoded in the antisense strand of DNA, can interact with significant affinity and selectivity with their corresponding sensepeptides. Experimentally, sense-antisense peptide recognition has been observed repeatedly. However, skepticism about the biological relevance of this phenomenon has persisted. This is due in part to the unexpected and somewhat couterintutive nature of the interaction as well as to its non-universality as an empirical observation. Nonetheless, antisense peptides in several cases investigated so far have been used as immobilized ligands for the successful affinity chromatographic separation of native (sense) peptides and proteins. For example, immobilized antisense peptides corresponding to Arg8-vasopressin (AVP) have been used to separate vasopressin from oxytocin chromatographically as well as to affinity capture AVP-receptor complex. These results, together with improved understanding of the general features of amino acid sequence which drive antisense-sense peptide interactions as well as new ideas for making antisense peptides chimeras, are beginning to suggest improved ways to make antisense-related peptides as affinity agents for separation as well as for other biotechnology applications.     

An algorithm for interpretation of low-energy collision-induced dissociation product ion spectra for de novo sequencing of peptides

An algorithm for interpretation of product ion spectra of peptides generated from ion trap mass spectrometry is developed for de novo amino acid sequencing of peptides for the purpose of protein identification. It is based on a multi-pass analysis of product ion data using a rigorous data extraction and sequence interpretation protocol in the initial pass. The extraction/interpretation algorithm becomes more relaxed in subsequent passes, considering more of the fragment ions, and potentially more sequence candidates. The possible peptide sequences generated by the algorithm are scored according to those sequences which best explain the fragment ion spectrum. These sequences are searched against a protein database using a BLAST search engine to find likely protein candidates. The method is also suitable for locating and determining protein modifications, and can be applied to de novo interpretation of peptide fragment ions in the tandem mass (MS/MS) spectrum produced from a mixture of two peptides having similar nominal mass, but different sequences. Using a known protein, bovine serum albumin, as an example, it is illustrated that this method is rapid and efficient for MS/MS spectral interpretation. This method combined with BLAST programs is then applied to search homologies and to generate information on post-translational modifications of an unknown protein isolated from shark cartilage that does not have a complete genome or proteome database.     

Mixed-mode hydrophilic interaction/cation-exchange chromatography: separation of complex mixtures of peptides of varying charge and hydrophobicity

Mixed-mode hydrophilic interaction/cation-exchange chromatography (HILIC/CEX) was applied to the separation of two mixtures of synthetic peptide standards: (i) a 27-peptide mixture containing three groups of peptides (each group containing nine peptides of the same net charge of +1, +2 or +3), where the hydrophilicity/hydrophobicity of adjacent peptides within the groups varied only subtly (generally by only a single carbon atom); and (ii) peptide pairs with the same composition but different sequences, where the sole difference between the peptides was the position of a single amino acid substitution. HILIC/CEX is essentially CEX chromatography in the presence of high levels of organic modifier (generally ACN). The present study demonstrated the dramatic effect of increasing ACN concentration (optimum levels of 60-80%, depending on the application) on the separation of both mixtures of peptides. The greater the charge on the peptides, the better the separation achievable by HILIC/CEX. In addition, HILIC/CEX separation of both the peptide mixtures used in the present study was shown to be superior to that of the more commonly applied RP-HPLC mode. Our results highlight again the efficacy of HILIC/CEX as a peptide separation mode in its own right as well as an excellent complement to RP-HPLC.     

Two-stage Off-Gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma

This paper presents the recently introduced Off-Gel electrophoresis (OGE) technology as a versatile tool to reproducibly fractionate intact proteins and peptides into discrete liquid fractions. The coupling of two stages of OGE, i.e., the separation of intact proteins in a first-stage followed by fractionation of peptides derived from each protein fraction after proteolysis in a second stage, results in an array of 15 x 15 fractions that are directly amenable to additional peptide fractionation like reverse-phase liquid chromatography (RPC). The analysis of all second-stage peptide fractions from only the first-stage protein fraction representing pH 5.0 -5.15 by on-line reverse-phase LC-tandem mass spectrometry resulted in the identification of 53 proteins (337 peptides), of which 10 were on different immunoglobulin (Ig) chains, with an input of only 1.5 mg human blood plasma proteins. Increasing the protein load to approximately 12 mg increased the number of identified proteins in the same protein fraction to 73 proteins (449 peptides), of which 15 were Ig-related. Immunodepletion of six of the most abundant proteins (albumin, transferrin, haptoglobin, IgG, IgA, and alpha-1-antitrypsin) prior to first-stage OGE with an input of 1.5 mg of protein (equivalent to approximately 10 mg nondepleted plasma) resulted in the identification of 81 proteins (660 peptides), of which three were still Ig fragments. The pI-based separation of peptides appears to be nonuniform based on the theoretically determined pI values of identified peptides. This observation specifically accounts for the neutral zone (pI 5-8) and can be accounted for by the physicochemical properties of the peptides given by their amino acid composition. The power of OGE separation of proteins and peptides is discussed with a focus on the use of the knowledge about the pI of proteins and peptides that assist the validation of correct identifications together with the retention time of peptides on RPC.     

Studies on Fragmentation of Peptide by Nano-electrospray Ionization Fourier Transform Ion Cyclotron Resonance Multi-stage Tandem Mass Spectrometry

The sequence analysis of peptides was performed by nano-electrospray ionization Fourier transform ion cyclotron resonance tandem mass spectrometry(Nano-ESI-FT-ICR-MSn) and several peptides were chosen as examples. With the aid of the collision induced dissociation(CID), FT-ICR provides not only precise mass/charge ratio, but also structure information of the selected peptides. The fragment ions were identified according to the observed molecular weights and peptide sequence was determined successfully. So Nano-ESI-FT-ICR-MSn is a useful tool for identification of the amino acid sequence of peptides with high confidence. Besides, a pathway for the dehydration of y ions without amino acids containing carboxylic acid under sustained off-resonance irradiation collision-induced dissociation(SORI-CID) condition was proposed.     

Applicability of the critical chromatography concept to proteomics problems: Experimental study of the dependence of peptide retention time on the sequence of amino acids in the chain

Experimental data on the separation of synthetic and natural peptides are presented as treated in terms of the separation model proposed by the authors, which allows for the chain connectivity of amino acid residues and the cooperative character of their interaction with the surface. It was shown that the model accurately predicts the separation of peptides with identical amino acid contents and different sequences of units in the chain. The differences in the sequence may be permutation of amino acid residues and the presence of terminal groups, amino acid isomers, or mirror sequences in the chain. The separation model was used to predict the retention times of peptides prepared via the enzymatic hydrolysis of E. coli proteins and bovine serum albumin with trypsin. It was shown that in general the model accurately explains the array of experimental data on the separation of such peptides, thus being the first successful attempt to relate the chain sequence to the retention volume.     

Determination of the enantiomeric purity of synthetic peptides by gas chromatography-mass spectrometry.

Hydrolysis using 2H-labelled HCl and H2O, derivatization of free amino acids as N.O.S-trifluoroacetyl isobutyl esters, separation by gas chromatography on a chiral stationary phase and detection by mass spectrometry in selected-ion monitoring mode have been used in order to determine the enantiomeric purity of several synthetic peptides. Chromatographic separation has been optimized for proline, whose two enantiomers are difficult to resolve under standard conditions. Electron impact and methane chemical ionization mass spectra and chromatographic resolution of unnatural amino acids, such as 3-(1-naphthyl)-alanine and p-chlorophenylalanine, are reported. For both natural and unnatural amino acids selected-ion monitoring of the different fragmentation peaks has been carried out. The results are interpreted from the point of view of whether or not the fragments contain a hydrogen atom on the alpha-carbon, and a comparison between electron impact and methane chemical ionization has been carried out. The main advantage of the latter method is that a quasimolecular ion can be observed for all the amino acids studied.     

超高效液相色谱-串联质谱法测定阿胶中马、牛、羊、猪、骆驼、鹿皮源成分

建立了阿胶中马、牛、羊、猪、骆驼、鹿皮源成分的检测方法。通过比对驴皮和马皮、牛皮、猪皮、羊皮、骆驼皮、鹿皮胶原蛋白的序列,采用蛋白酶切技术和高分辨质谱技术发现理论的各杂皮胶原蛋白特征肽。同时建立三重四极杆质谱筛查方法,以含0.1%（v/v）甲酸的乙腈溶液和0.1%（v/v）甲酸水溶液作为流动相,梯度洗脱,电喷雾离子源（ESI）正离子扫描模式,多反应监测。15批阿胶样品检出了杂皮源成分。该方法操作简便,专属性强,可用于阿胶中杂皮源成分的鉴别,并已成功用于阿胶日常打假监督抽验工作。