Microsequences of 145 proteins recorded in the two-dimensional gel protein database of normal human epidermal keratinocytes.

Microsequencing of proteins recovered from two-dimensional (2-D) gels is being used systematically to identify proteins in the master human keratinocyte 2-D gel database. To date, about 250 protein spots recorded in human 2-D gel databases have been microsequenced and, of these, 145 are recorded in the keratinocyte database under the entry partial amino acid sequence. Coomassie Brilliant Blue-stained protein spots cut from several (up to 40) dry gels were concentrated by elution-concentration gel electrophoresis, electroblotted onto PVDF membranes and digested in situ with trypsin. Eluting peptides were separated by reversed-phase HPLC, collected individually and sequenced. Computer search using the FASTA and TFASTA programs from Genetics Computer Group indicated that 110 of the microsequenced polypeptides shared significant similarity with proteins contained in the PIR, Mipsx or GenEMBL databases. Only 35 polypeptides corresponded to hitherto unknown proteins. Peptide sequences of all 145 proteins are listed together with their coordinates (apparent molecular weight and pI) in the keratinocyte database.     

Separation of peptides on a polystyrene resin column

A high-performance liquid chromatographic column of porous spherical polystyrene--divinylbenzene copolymer (Hamilton PRP-1) was found to be useful for reversed-phase resolution of a wide range of peptides. Recoveries and resolution were comparable with those from more widely used alkyl silica-based columns. Tests involving more than 40 peptides, ranging from 2 to 34 residues, and 3 proteins, indicated wide applicability of this column. The retention times of peptides of known composition are predicted. The stability of the resin at high pH permits protocols of separation involving successive chromatograms at widely different pH values, and offers a second dimension to the resolving power of a single column.     

Identification of proteins from membrane preparations by a combination of MALDI TOF-TOF and LC-coupled linear ion trap MS analysis of an Antarctic bacterium Pseudomonas syringae Lz4W, a strain with unsequenced genome

Multidimensional protein identification technology helps in identifying a large number of proteins with ESI by sequencing several peptides with MS/MS methods. When ionization and separation of different hydrophobic and hydrophilic peptides in a single process are difficult, a combination of LC-coupled linear ion trap MS and MALDI TOF/TOF can be used for identification of proteins as shown in the present study. We have used this combinational approach to identify membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, which are separated by SDS gel electrophoresis. Although the genome of P. syringae Lz4W has not been sequenced, the known genome sequences of mesophilic Pseudomonas species have been used for the identification of the proteins. Broadly, many membrane proteins, proteins with a wide range of molecular weight and pI including some integral membrane proteins could be identified using this procedure. Some of the identified proteins are involved in low temperature adaptation.     

Nanoparticle-stabilized colloids in compressible hydrofluoroalkanes

In this work, we show that nanoparticles (NPs) dispersed in compressible hydrofluoroalkanes (HFAs) at small volume fractions are capable of stabilizing micrometer-sized particle colloids, which otherwise flocculate due to strong van der Waals forces. Water-soluble, biodegradable NPs with a chitosan (CS) core, grafted with highly HFA-philic moieties, can be readily dispersed in the low dielectric HFAs and are capable of imparting stability to a wide range of therapeutic particles having different chemistries (polar or hydrophobic; small and large molecular weight, including peptides and proteins) and morphologies (micronized crystals or amorphous). These NP systems thus serve as a broadly applicable platform for the noninvasive delivery of therapeutics to and through the lungs using propellant-based, portable inhalers, and are also of potential relevance in other industries where HFAs are employed as solvents or propellants. This concept may also be applicable to other compressible solvents.     

The effect of sodium dodecyl sulfate and Pluronic F127 on the electrophoretic separation of protein and polypeptide test mixtures at acid pH

Using a test mixture consisting of standard proteins (cytochrome c, chymotrypsinogen A, hen egg albumin, bovine serum albumin, aldolase, catalase and ferritin) and synthetic polypeptides (polylysine, polyaspartic, polyglutamic acid and polyproline) it was revealed that using sodium dodecyl sulfate (SDS) as background electrolyte modifier at acid pH (2.5) allows selective separation of highly positively charged polypeptides (polylysine) provided that their relative molecular mass is sufficiently low (3300 Da). The altered elution sequence of standard proteins as compared to a separation done without SDS may help their identification. Addition of Pluronic F127 offers clear-cut separations of standard proteins up to a relative molecular mass of 5 x 10(4) Da and allows to reveal protein/polypeptide microheterogeneity where applicable. None of the systems tested is suitable for the separation of acidic polypeptides and polyproline.     

Analysis of salivary peptides using HPLC-electrospray mass spectrometry

Salivary peptides are involved in a wide range of functions constituting the first line of defence of oral cavity and precursors of dental pellicle formation. The presence of mucins in saliva makes difficult the analysis of the proteic content. This is due mainly to aggregation phenomenon between mucins and other high molecular weight glycoproteins and salivary proteins. Considering the importance of salivary peptides in biological functions, we have evaluated the influence of four different extraction methodologies on the separation and identification of these proteins by HPLC-MS. Based on their molecular weight, we identified a total of 22 peptides when extraction was performed using a solution of guanidine (6 m), compared with 14 peptides identified when saliva is acidified with TFA, which is an often used procedure. Our results also show the presence of mucin bind peptides, which include statherin, PRP1, PRP3, Histatin 1 and Histatin 5.     

Stationary and mobile phases in hydrophilic interaction chromatography: a review

Hydrophilic interaction chromatography (HILIC) is valuable alternative to reversed-phase liquid chromatography separations of polar, weakly acidic or basic samples. In principle, this separation mode can be characterized as normal-phase chromatography on polar columns in aqueous-organic mobile phases rich in organic solvents (usually acetonitrile). Highly organic HILIC mobile phases usually enhance ionization in the electrospray ion source of a mass spectrometer, in comparison to mobile phases with higher concentrations of water generally used in reversed-phase (RP) LC separations of polar or ionic compounds, which is another reason for increasing popularity of this technique. Various columns can be used in the HILIC mode for separations of peptides, proteins, oligosaccharides, drugs, metabolites and various natural compounds: bare silica gel, silica-based amino-, amido-, cyano-, carbamate-, diol-, polyol-, zwitterionic sulfobetaine, or poly(2-sulphoethyl aspartamide) and other polar stationary phases chemically bonded on silica gel support, but also ion exchangers or zwitterionic materials showing combined HILIC-ion interaction retention mechanism. Some stationary phases are designed to enhance the mixed-mode retention character. Many polar columns show some contributions of reversed phase (hydrophobic) separation mechanism, depending on the composition of the mobile phase, which can be tuned to suit specific separation problems. Because the separation selectivity in the HILIC mode is complementary to that in reversed-phase and other modes, combinations of the HILIC, RP and other systems are attractive for two-dimensional applications. This review deals with recent advances in the development of HILIC phase separation systems with special attention to the properties of stationary phases. The effects of the mobile phase, of sample structure and of temperature on separation are addressed, too.     

梯度加压毛细管电色谱分离蛋白质

 以1.5 μm无孔硅胶颗粒(non-porous silica,NPS)为固定相,采用电压和压力联合驱动流动相,用反相梯度加压毛细管电色谱(p-CEC)在7.5 min内实现了核糖核酸酶A、细胞色素C、溶菌酶和肌红蛋白等4种蛋白质的快速、高效的分离。比较了梯度加压毛细管电色谱和微柱液相色谱(μ-HPLC)分离蛋白质的结果,同时考察了固定相、离子对试剂三氟醋酸(TFA)浓度和电压等条件对梯度加压毛细管电色谱分离蛋白质的影响。结果表明,梯度p-CEC可以通过调节电压精细调节带电溶质的保留,提高分离选择性,缩短分离时间,得到较高的柱效。该方法在蛋白质分离分析及蛋白质组学的研究中具有很大的应用潜力，为高效快速地分离蛋白质开辟了新的途径。     

An Estimation Technique of Molecular Weights of Bio-Oligomers by Reversed-Phase Liquid Chromatography

Abstract

A new simple and accurate method for molecular weight estimation of oligomers by reversed-phase liquid chromatography was developed and has been proposed to use in the investigation of bio-oligomers. Capacity factors (k′) of 24 peptides and proteins ranging in molecular weight from 200 to 70000 were measured independently under isocratic eluting conditions with slightly different acetonitrile contents in the mobile phase. Profiles of plots of the log k' values of the peptides and proteins against the acetonitrile contents were on straight lines with different slopes. These slopes were characteristic for each oligomer and found to be proportional to the two/thirds power of the molecular weight. This elution behavior of oligomers in reversed-phase liquid chromatography can be explained in terms of the solvophobic theory. The estimated molecular weights of several bio-oligomers were more accurate than those obtained by size-exclusion chromatography. when the range of molecular weights was limited from 10³ to 2×10⁴.     

Photo-Responsive Phase-Separating Fluorescent Molecules for Intracellular Protein Delivery

Cellular membranes, including the plasma and endosome membranes, are barriers to outside proteins. Various vehicles have been devised to deliver proteins across the plasma membrane, but in many cases, the payload gets trapped in the endosome. Here we designed a photo-responsive phase-separating fluorescent molecule ( PPFM ) with a molecular weight of 666.8 daltons. The PPFM compound condensates as fluorescent droplets in the aqueous solution by liquid-liquid phase separation ( LLPS ), which disintegrate upon photoirradiation with a 405 nm light-emitting diode ( LED ) lamp within 20 min or a 405 nm laser within 3 min. The PPFM coacervates recruit a wide range of peptides and proteins and deliver them into mammalian cells. Photolysis disperses the payload from condensates into the cytosolic space. Altogether, a type of small molecules that are photo-responsive and phase separating are discovered; their coacervates can serve as transmembrane vehicles for intracellular delivery of proteins, whereas photo illumination triggers the cytosolic distribution of the payload.     

毛细管电泳-质谱联用技术及其在蛋白质组学中的应用

蛋白质组学研究在生物学、精准医学等方面发挥着重要的作用。然而研究面临的巨大挑战来自生物样品的复杂性,因此在质谱（MS）鉴定技术不断革新的同时,发展分离技术以降低样品复杂度尤为重要。毛细管电泳（CE）技术具有上样体积小、分离效率高、分离速度快等优势,其与质谱的联用在蛋白质组学研究中越来越受到关注。低流速鞘流液和无鞘流液接口的发展及商品化推动了CE-MS技术的发展。目前毛细管区带电泳（CZE）、毛细管等电聚焦（CIEF）、毛细管电色谱（CEC）等分离模式已与质谱联用,其中CZE-MS应用最广泛。目前被广泛采用的蛋白质组学研究策略主要是基于酶解肽段分离鉴定的"自下而上（bottom-up）"策略。首先,CE-MS技术对酶解肽段的检测灵敏度高达1 zmol,已成功应用于单细胞蛋白质组学;其次,毛细管电泳技术与反相液相色谱互补,为疏水性质相近的肽段（尤其是翻译后修饰肽段）的分离鉴定提供了新的途径。基于整体蛋白质分离鉴定的自上而下"top-down"策略可以直接获得更精准、更完整的蛋白质信息。CE技术在蛋白质大分子的分离方面具有分离效率高、回收率高的优势,其与质谱的联用提高了整体蛋白质的鉴定灵敏度和覆盖度。非变性质谱（native MS）是一种在近生理条件下从完整蛋白质复合物水平上进行分析的质谱技术。CE与非变性质谱联用已被尝试用于蛋白质复合体的分离鉴定。该文引用了与CE-MS和蛋白质组学应用相关的93篇文献,综述了以上介绍的CE-MS的研究进展以及在蛋白质组学分析中的应用优势,并总结和展望了其应用前景。     

万古霉素手性固定相的制备与对映体分离研究

采用双官能团试剂4,4′-二苯基甲烷二异氰酸酯在无水二甲基甲酰胺(DMF)中直接与大环糖肽类抗生素万古霉素及γ-氨丙基硅胶键合,得到环状抗生素手性固定相(CSP)并用于高效液相色谱手性分析。实验结果证实,合成的万古霉素CSP在正相和反相条件下均有一定的拆分能力,其中在反相条件下拆分了17种对映体,显示出其较为广泛的拆分范围,且磷酸缓冲体系略优于三乙胺-乙酸缓冲体系;对一些物质,如D,L-丹酰化氨基酸的拆分有一定的规律,能给出绝对构型信息。所制备的CSP在相体系转化时不发生老化和变性,显示了一定的稳定性。对该CSP的拆分机理进行分析所得到的结果与Armstrong等的分析结果基本一致。     

Hydrophilic-interaction chromatography of peptides on hydrophilic and strong cation-exchange columns

Hydrophilic-interaction chromatography (HILIC) was recently introduced as a potentially useful separation mode for the purification of peptides and other polar compounds. The elution order of peptides in HILIC, which separates solutes based on hydrophilic interactions, should be opposite to that obtained in reversed-phase chromatography, which separates solutes based on hydrophobic interactions. Three series of peptides, two of which consisted of positively charged peptides (independent of pH at pH less than 7) and one of which consisted of uncharged or negatively charged peptides (dependent on pH), and which varied in overall hydrophilicity/hydrophobicity, were utilized to examine the separation mechanism and efficiency of HILIC on hydrophilic and strong cation-exchange columns.     

Proteomic analysis of rat plasma by two-dimensional liquid chromatography and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

The proteomic analysis of plasma and serum samples represents a formidable challenge due to the presence of a few highly abundant proteins such as albumin and immunoglobulins. Detection of low abundance protein biomarkers therefore requires either the specific depletion of high abundance proteins using immunoaffinity columns and/or optimized protein fractionation methods based on charge, size or hydrophobicity. Here we describe a two-dimensional (2D) liquid chromatography separation method for the fractionation of rat plasma. In the first dimension proteins were separated by chromatofocusing according to their isoelectric point (pI). In the second dimension, proteins were further fractionated by non-porous, reversed-phase chromatography according to their hydrophobicity. The data from both separations was displayed as a 2D protein expression map of pI versus retention time (relative hydrophobicity). Both separations were carried out on the ProteomeLab PF 2D system (Beckman Coulter), an instrument platform that provides a high degree of automation and real-time monitoring of the separation process. The reproducibility of the first-dimension separation was evaluated in terms of pH gradient formation. The second-dimension separation was evaluated in terms of peak retention times on the reversed-phase column. We found in four consecutive chromatofocusing separations that the pH gradient differed by less than 0.2 pH units at any time during the elution step. Second dimension retention times of peaks from identical pI fractions differed by less than 7 s in six consecutive separations. Each 2D separation generated a total of 540 fractions which were analyzed by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). We detected approximately 275 peptides and proteins with molecular masses ranging from 3 to 225 kDa. Most fractions were found to contain multiple low and high molecular weight proteins. Differential display of 2D protein expression maps from retinol-sufficient and -deficient rat plasma samples identified a fraction with several proteins that appeared to be down-regulated in the vitamin A-deficient animal. Quantitative proteomic analysis of complex samples such as plasma is still a difficult task. We discuss the potential of this approach for biomarker discovery and address the experimental challenges that remain.     

用于人血浆中蛋白质分离的在线阵列式二维常规柱液相色谱系统的建立

构建了一种在线阵列式二维常规柱液相色谱系统,并将其应用于分离血浆中的完整蛋白质。该系统以1根强阴离子交换柱作为第一维分离柱,8根阵列式反相色谱柱作为第二维分离柱。强阴离子交换柱分离的馏分通过十通阀被依次转移到第二维预柱上并得到保留富集,随后第二维流动相通过分流器同时将预柱上的蛋白质反冲至分析柱上进行分离。二维之间以及第二维阵列色谱柱之间均相互独立,从而可以提高系统分离的通量和总峰容量。采用该系统对血浆中的蛋白质进行了完整蛋白质水平上的分离。该系统具有高通量和高分辨率的特点,为血浆样品中高丰度蛋白质的去除以及血浆样品的深入研究提供了一种有效的手段。     

Separation of proteins from human plasma by sample displacement chromatography in hydrophobic interaction mode

Sample displacement chromatography (SDC) in reversed-phase and ion-exchange modes was introduced approximately 20 years ago. This method was first used for the preparative purification of peptides and proteins. Recently, SDC in ion-exchange mode was also successfully used for enrichment of low-abundance proteins from human plasma. In this paper, the use of SDC for the separation of plasma proteins in hydrophobic interaction mode is demonstrated. By use of two or more columns coupled in series during sample application, and subsequent elution of detached columns in parallel, additional separation of bound proteins was achieved. Further low-abundance, physiologically active proteins could be highly enriched and detected by ESI-MS/MS.     

Monitoring free silanols on reversed-phase supports with peptide standards

Summary A series of synthetic peptide HPLC standards has been designed for use in monitoring free silanols on silica-based reversed-phase supports. The four standards (+ 1 to + 4 net charge) showed great versatility in monitoring silanol activity over a pH range of 2.0 to 7.0. We have developed a silanol monitoring system based on the sensitivity of the standards to ionic interactions with reversed-phase packings at pH 7.0. This monitoring procedure involves chromatographing the peptides at pH 7.0 with a combined acetonitrile and sodium perchlorate linear AB gradient and is generally applicable to reversed-phase packings exhibiting a wide range of silanol concentrations. These standards not only demonstrate the presence and extent of free silanols, they also allow the researcher to determine what changes must be made to the mobile phase composition to minimize ionic interactions. In addition, the standards, in conjunction with the double gradient monitoring system at pH 7.0, will aid researchers and manufacturers in the improvement and development of reversed-phase matrices.     

一种规模化蛋白质组分离和鉴定新方法研究及其应用

建立了一种规模化的蛋白质组分离和鉴定新方法。通过对在生命发育过程中具有重要研究价值的人胎肝线粒体蛋白质组的分离分析，表明与毛细管液-质联用的不同分离方法的组合可以增大检测动态范围和分辨率。研究共鉴定了2977个肽段，归属于915种蛋白质。去除批次间冗余后，鉴定的蛋白质为477种，其中291种为唯一蛋白质，186种为蛋白质簇，144种蛋白质明确定位于人胎肝线粒体中。所鉴定蛋白质的分子量分布范围为7000Da～330000 Da，pI值分布在4．0～11．89，克服了两维凝胶电泳在分子量和pH方面的歧视性问题。实验中发现的蛋白质簇以及确定一种蛋白质需要最少肽段数的问题还需要进一步研究。     

Capillary electrophoresis of cationic random coil peptide standards: effect of anionic ion-pairing reagents and comparison with reversed-phase chromatography

The present study compares a charge/hydrophobicity capillary electrophoresis (CE) approach to reversed-phase high-performance liquid chromatography (RP-HPLC) for the separation of three series of four synthetic, random coil peptide standards. Each series has peptides of the same positive charge (+1, +2 and +3 series) and length but differing in hydrophobicity. Complete resolution of the 12 peptides was achieved via a novel CE approach: a capillary zone electrophoresis (CZE) mode effected a separation of identically charged peptides; within each charged group of peptides, the addition of perfluorinated acid anionic ion-pairing reagents allowed resolution of the peptides through a mechanism based on peptide hydrophobicity which we have termed ioninteraction (II)-CZE. The peak capacity and peptide resolution of this CE approach was superior to that of RP-HPLC and stresses an important role for CE for peptide/proteomic applications.     

Temperature selectivity effects in reversed-phase liquid chromatography due to conformation differences between helical and non-helical peptides

In order to characterize the effect of temperature on the retention behaviour and selectivity of separation of polypeptides and proteins in reversed-phase high-performance liquid chromatography (RP-HPLC), the chromatographic properties of four series of peptides, with different peptide conformations, have been studied as a function of temperature (5-80 degrees C). The secondary structure of model peptides was based on either the amphipathic alpha-helical peptide sequence Ac-EAEKAAKEX(D/L)EKAAKEAEK-amide, (position X being in the centre of the hydrophobic face of the alpha-helix), or the random coil peptide sequence Ac-X(D/L)LGAKGAGVG-amide, where position X is substituted by the 19 L- or D-amino acids and glycine. We have shown that the helical peptide analogues exhibited a greater effect of varying temperature on elution behaviour compared to the random coil peptide analogues, due to the unfolding of alpha-helical structure with the increase of temperature during RP-HPLC. In addition, temperature generally produced different effects on the separations of peptides with different L- or D-amino acid substitutions within the groups of helical or non-helical peptides. The results demonstrate that variations in temperature can be used to effect significant changes in selectivity among the peptide analogues despite their very high degree of sequence homology. Our results also suggest that a temperature-based approach to RP-HPLC can be used to distinguish varying amino acid substitutions at the same site of the peptide sequence. We believe that the peptide mixtures presented here provide a good model for studying temperature effects on selectivity due to conformational differences of peptides, both for the rational development of peptide separation optimization protocols and a probe to distinguish between peptide conformations.