蛋白质高效分离两维色谱柱的选择优化

为了构建高效的离子交换/反相二维液相色谱(IEC/RPLC)分离平台系统,提高复杂蛋白质样品的分离效率,对色谱柱进行了评价与筛选。通过对实际人肝蛋白质样品的分离效果的比较,选择确定了TSKgel DEAE-5PW弱阴离子交换色谱柱(WAX)作为第一维色谱分离柱;考察了同一规格的10支代表性反相色谱柱(250 mm×4.6 mm, 5 μm, 30 nm, C4、C8或C18),通过评价其对尿嘧啶、硝基苯、萘和芴的分离性能以及对3种标准蛋白质样品的非特异性吸附、对人肝蛋白质样品的WAX馏分的分离效果,最终确定以Jupiter 300 C4反相色谱柱作为第二维色谱分离柱。对两维色谱柱的选择优化为蛋白质高效分离二维液相色谱平台的搭建提供了可靠基础。     

Evaluation of different two‐dimensional chromatographic techniques for proteomic analysis of mouse cardiac tissue

In proteomics experiments the first critical step after sampling is certainly sample preparation. Multidimensional chromatography techniques have emerged as a powerful tool for the large‐scale analysis of such complex samples as biological samples. In order to evaluate these separation techniques, microgram quantities of protein extracted from mouse heart tissue were fractionated by four different chromatographic methods. Regarding peptide‐level fractionation, the first dimension of separation was performed with high‐pH reversed‐phase chromatography (pH‐RP) and strong cation exchange chromatography (SCX). Regarding protein‐level fractionation, C₈ protein reversed‐phase (C₈‐RP Prot) and high‐recovery protein reversed‐phase (hr‐RP Prot) were used instead. The second dimension consisted of a reversed‐phase nano‐HPLC on‐Chip coupled to an electrospray ionization quadrupole time‐of‐flight mass spectrometer for tandem mass spectrometric analysis. The performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The peptide‐level pH‐RP and the hr‐RP Prot protein‐level separations were the best methods, identifying 1338 and 1303 proteins, respectively. The peptide‐level SCX, with 509 proteins identified, was the worst method. Copyright © 2010 John Wiley & Sons, Ltd.     

Analytical methods for the characterization of proteins and peptides in wines

Although proteins and peptides are minor constituents of wine, they make a significant contribution to its quality. Proteins can cause a number of technological problems during vinification and may be responsible for the appearance of turbidity in bottled wine. Peptides exhibit surfactant and sensory properties that can influence the organoleptic characteristics of wine. These reasons make protein and peptide analysis a necessity. In this paper, some of the applications in sample preparation, electrophoretic and chromatographic analysis, and detection of proteins and peptides in wine are examined. Special attention is paid to the methodologies that the authors have used in previously published studies, in some cases developed by them, and in other cases taken from the literature and used routinely in their laboratory.     

Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling

Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.     

Characterization of copolymers of polycarbonate and polydimethylsiloxane by 2D chromatographic separation,MALDI-TOF mass spectrometry,and FTIR spectroscopy

Abstract

The structure and composition of polycarbonate polydimethylsiloxane copolymer (PC-co-PDMS) was investigated by applying various analytical approaches including chromatographic separation methods, spectrometric, and spectroscopic detection techniques. In particular, size exclusion chromatography (SEC) and liquid adsorption chromatography operating at different conditions (e.g. using gradient solvent systems) were used to achieve separations according to molar mass and functionality distribution. The coupling of both techniques resulted in fingerprint two-dimensional plots, which could be used to easily compare different copolymer batches. Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry was applied for structural investigations. The different ionization behavior of both comonomers, however, strongly limited the applicability of this technique. In contrast to that, Fourier-transform Infrared (FTIR) spectroscopy could be used to quantify the amount of PDMS in the copolymer at different points in the chromatogram. The resulting methodology was capable of distinguishing PC-co-PDMS copolymer from PC homopolymer chains present in the material.     

Characterization of quinoa seed proteome combining different protein precipitation techniques: Improvement of knowledge of nonmodel plant proteomics

A shotgun proteomics approach was used to characterize the quinoa seed proteome. To obtain comprehensive proteomic data from quinoa seeds three different precipitation procedures were employed: MeOH/CHCl₃/double‐distilled H₂O, acetone either alone or with trichloroacetic acid; the isolated proteins were then in‐solution digested and the resulting peptides were analyzed by nano‐liquid chromatography coupled to tandem mass spectrometry. However, since quinoa is a nonmodel plant species, only a few protein sequences are included in the most widely known protein sequence databases. To improve the data reliability a UniProt subdatabase, containing only proteins of Caryophillales order, was used. A total of 352 proteins were identified and evaluated both from a qualitative and quantitative point of view. This combined approach is certainly useful to increase the final number of identifications, but no particular class of proteins was extracted and identified in spite of the different chemistries and the different precipitation protocols. However, with respect to the other two procedures, from the relative quantitative analysis, based on the number of spectral counts, the trichloroacetic acid/acetone protocol was the best procedure for sample handling and quantitative protein extraction. This study could pave the way to further high‐throughput studies on Chenopodium Quinoa.     

Comparison of gas chromatographic and gas chromatographic/mass spectrometric techniques for the analysis of TNT and related nitroaromatic compounds

The use of capillary column gas chromatography and gas chromatography/mass spectrometry for the analysis of a series of standard solutions (0.1 to 10 μg/ml) of 2,4,6-trinitrotoluene (TNT) and eight other nitroaromatic components was evaluated. The techniques included gas chromatography with electron capture detection (GC/ECD), full scan and selected ion monitoring gas chromatography/mass spectrometry with electron impact ionization (EI/FS and EI/SIM), full scan and selected ion monitoring gas chromatography/mass spectrometry with positive ion chemical ionization using methane reagent gas (PICI/FS and PICI/SIM), and full scan and selected ion monitoring gas chromatography/mass spectrometry with negative ion chemical ionization using methane reagent gas (NICI/FS and NICI/SIM). The performance of the techniques was comapared by determining the linear response range, precision, and detection limits of the analyses.     

Recent advances in proteolysis and peptide/protein separation by chromatographic strategies

This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chroma-tographic strategies in the past ten years, covering the main research in these areas especially in China. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hour...     

比较纳升反相色谱-串联质谱与毛细管区带电泳-串联质谱用于自顶向下蛋白质组学

自顶向下蛋白质组学的一个重要难题是缺乏与质谱可以在线连用并且可以提供高效蛋白质分离的液相分离技术。毛细管区带电泳与纳升反相色谱都可以与质谱在线连用,并且在复杂蛋白质样品分析方面也都有了显著的提升。在这里,我们首次比较了先进的纳升反相色谱-串联质谱与毛细管区带电泳-串联质谱平台用于自顶向下蛋白质组学分析。相对于纳升反相色谱-质谱而言,毛细管区带电泳-质谱可以将标准蛋白质样品的消耗量降低10倍,而且保持与纳升反相色谱-质谱相当的蛋白质信号强度。有意思的是,与毛细管区带电泳-质谱相比,纳升反相色谱-质谱可以获得更高的蛋白质分子的气相价态。这个现象可能是由于反相流动相中的高浓度乙腈使得蛋白质变性的更加充分。从1微克的大肠杆菌蛋白质样品中,毛细管区带电泳-串联质谱可以鉴定到159个蛋白质和513个蛋白质变体,而纳升反相色谱-串联质谱仅鉴定到105个蛋白质和277个蛋白质变体。当将大肠杆菌蛋白质的上样量提高到8微克时,纳升反相色谱-串联质谱可以鉴定到245个蛋白质和1004个蛋白质变体。由于纳升反相色谱-串联质谱具有比毛细管区带电泳-串联质谱更高的上样量与更宽的分离窗口,当蛋白质样品量不受限制时,纳升反相色谱-串联质谱具有明显的优势。但是,在痕量样品分析方面,毛细管区带电泳-串联质谱具有更大的潜力。     

疏水型色谱饼对人血清蛋白质组学样品的快速分离与制备

建立了疏水型色谱饼(10 mm×20 mm i.d.)与反相色谱(RPLC)离线二维色谱快速分离制备人血清蛋白质组学样品,并用基体辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)进行检测的方法。以4种标准蛋白质的稀溶液为模型进行分离富集,得到细胞色素c(Cyt-c)与肌红蛋白(Myo)的检出限均为1 pmol/μL,溶菌酶(Lys)和胰岛素（Ins）的检出限为0.1 pmol/μL。将此方法用于人血清蛋白质组学样品的分离与制备,随着血清处理量的增大,质谱可检出的组分数目与信号强度均增加,当血清处理量达到1.0 mL时,可检出低丰度蛋白质或多肽285个(相对分子质量均在15000以下)。研究中将1 μg Cyt-c加入到0.5 mL血清中,用上述方法在分离富集低丰度Cyt-c上取得了很好的效果。结果表明,采用疏水型色谱饼与反相色谱联用技术不仅可对血清样品中低丰度蛋白质进行有效的分离和富集,而且一次样品的处理量大,可显著提高低丰度蛋白质的分析、检测水平。     

分离分析技术在蛋白质组学研究中应用的新进展

蛋白质组学研究的核心技术之一是分离分析方法。该综述重点评述了分离分析技术在蛋白质组学研究,即在蛋白质组表达谱构建、翻译后修饰蛋白质组研究、蛋白质复合体和相互作用研究、蛋白质组定量研究中应用的新进展,介绍了各种分离分析方法的优点、应用范围和有待解决的问题。引用文献89篇。     

Polymer architectures via mass spectrometry and hyphenated techniques: A review

This review covers the application of mass spectrometry (MS) and its hyphenated techniques to synthetic polymers of varying architectural complexities. The synthetic polymers are discussed as according to their architectural complexity from linear homopolymers and copolymers to stars, dendrimers, cyclic copolymers and other polymers. MS and tandem MS (MS/MS) has been extensively used for the analysis of synthetic polymers. However, the increase in structural or architectural complexity can result in analytical challenges that MS or MS/MS cannot overcome alone. Hyphenation to MS with different chromatographic techniques (2D × LC, SEC, HPLC etc.), utilization of other ionization methods (APCI, DESI etc.) and various mass analyzers (FT-ICR, quadrupole, time-of-flight, ion trap etc.) are applied to overcome these challenges and achieve more detailed structural characterizations of complex polymeric systems. In addition, computational methods (software: MassChrom2D, COCONUT, 2D maps etc.) have also reached polymer science to facilitate and accelerate data interpretation. Developments in technology and the comprehension of different polymer classes with diverse architectures have significantly improved, which allow for smart polymer designs to be examined and advanced. We present specific examples covering diverse analytical aspects as well as forthcoming prospects in polymer science.     

Comparison of gas chromatographic hyphenated techniques for mercury speciation analysis

In this study, we evaluate advantages and disadvantages of three hyphenated techniques for mercury speciation analysis in different sample matrices using gas chromatography (GC) with mass spectrometry (GC-MS), inductively coupled plasma mass spectrometry (GC-ICP-MS) and pyrolysis atomic fluorescence (GC-pyro-AFS) detection. Aqueous ethylation with NaBEt(4) was required in all cases. All systems were validated with respect to precision, with repeatability and reproducibility <5% RSD, confirmed by the Snedecor F-test. All methods proved to be robust according to a Plackett-Burnham design for 7 factors and 15 experiments, and calculations were carried out using the procedures described by Youden and Steiner. In order to evaluate accuracy, certified reference materials (DORM-2 and DOLT-3) were analyzed after closed-vessel microwave extraction with tetramethylammonium hydroxide (TMAH). No statistically significant differences were found to the certified values (p=0.05). The suitability for water samples analysis with different organic matter and chloride contents was evaluated by recovery experiments in synthetic spiked waters. Absolute detection and quantification limits were in the range of 2-6 pg for GC-pyro-AFS, 1-4 pg for GC-MS, with 0.05-0.21 pg for GC-ICP-MS showing the best limits of detection for the three systems employed. However, all systems are sufficiently sensitive for mercury speciation in environmental samples, with GC-MS and GC-ICP-MS offering isotope analysis capabilities for the use of species-specific isotope dilution analysis, and GC-pyro-AFS being the most cost effective alternative.     

Optimum collision energies for proteomics: The impact of ion mobility separation

Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography–mass spectrometry (LC–MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC–MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values—giving the highest identification score—for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument—located before and after the IMS cell—were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).     

Multiresidue determination of quinolones regulated by the European Union in bovine and porcine plasma. Application of chromatographic and capillary electrophoretic methodologies

This paper presents the multiresidue determination of the series of quinolones regulated by the European Union (marbofloxacin, ciprofloxacin, danofloxacin, enrofloxacin, sarafloxacin, difloxacin, oxolinic acid and flumequine) in bovine and porcine plasma using capillary electrophoresis and liquid chromatography with ultraviolet detection (CE‐UV, LC‐UV), liquid chromatography–mass spectrometry and –tandem mass spectrometry (LC‐MS, LC‐MS/MS) methods. These procedures involve a sample preparation by solid‐phase extraction for clean‐up and preconcentration of the analytes before their injection into the separation system. All methods give satisfactory results in terms of linearity, precision, accuracy and limits of quantification. The suitability of the methods to determine quinolones was evaluated by determining the concentration of enrofloxacin and ciprofloxacin in real samples from pig plasma and cow plasma. Copyright © 2010 John Wiley & Sons, Ltd.     

Open source simulation tool for electrophoretic stacking,focusing, and separation

We present the development, formulation, and performance of a new simulation tool for electrophoretic preconcentration and separation processes such as capillary electrophoresis, isotachophoresis, and field amplified sample stacking. The code solves the one-dimensional transient advection-diffusion equations for multiple multivalent weak electrolytes (including ampholytes) and includes a model for pressure-driven flow and Taylor–Aris dispersion. The code uses a new approach for the discretization of the equations, consisting of a high resolution compact scheme which is combined with an adaptive grid algorithm. We show that this combination allows for accurate resolution of sharp concentration gradients at high electric fields, while at the same time significantly reducing the computational time. We demonstrate smooth, stable, and accurate solutions at current densities as high as 5000 A/m² using only 300 grid points, and a 75-fold reduction in computational time compared with equivalent uniform grid techniques. The code is available as an open source for free at http://microfluidics.stanford.edu.     

Interfaces for coupled liquid-phase separation/mass spectrometry techniques. An update on recent developments

An update is presented covering the latest developments in the interfacing of liquid-phase separation systems and mass spectrometers. The interfacing devices presented are those developed for continuous-flow matrix-assisted laser desorption/ionization, micro- and nano-liquid chromatography/masspectrometry (MS), capillary electrophoresis/MS and on-chip separation technologies/MS. From the information that can be found in the most recent literature on the topic, it is evident that the trend towards the miniaturization of separation and interface devices is gaining ground. This can be rationalized by the substantial gains in sensitivity for the detection and study of extremely low levels of analytes and especially of high molecular mass biopolymers.     

Steroid-estrogen determination in sediment and sewage sludge: a critique of sample preparation and chromatographic/mass spectrometry considerations, incorporating a case study in method development

Steroid estrogens have been identified in the solid matrices of unit treatment processes in sewage treatment works (STWs) and in sediments of watercourses that receive effluent. This article discusses the sample preparation and analytical considerations necessary for reliable determination and the need to evaluate for possible matrix interferences during method development. Complementing this is a case study highlighting the potential for analyte transformation during sample preparation and the phenomena of ion suppression when utilising LC/MS ESI with a comparison of method recoveries by GC/MS. We discuss the use of LC/MS/MS and TOF instruments; however, at present, their use in environmental analyses appears to be limited because of their capital costs.     

Identification evidence unraveled by strict proteomics rules toward forensic samples

Snake venom is a complex mixture of proteins and peptides secreted by venomous snakes from their poison glands. Although proteomics for snake venom composition, interspecific differences, and developmental evolution has been developed for a decade, current diagnosis or identification techniques of snake venom in clinical intoxication and forensic science applications are mainly dependent on morphological and immunoassay. It could be expected that the proteomics techniques directly offer great help. This work applied a bottom-up proteomics method to identify proteins’ types and species attribution in suspected snake venom samples using ultrahigh-performance liquid chromatography–quadrupole-electrostatic field Orbitrap tandem mass spectrometric technique, and cytotoxicity assay was amended to provide a direct evidence of toxicity. Toward the suspicious samples seized in the security control, sample pretreatment (in-sol and in-gel digestion) and data acquisition (nontargeted and targeted screening) modes complemented and validated each other. We have implemented two consequent approaches in identifying the species source of proteins in the samples via the points of venom proteomics and strict forensic identification. First, we completed a workflow consisting of a proteomics database match toward an entire SWISS-PROT (date 2018-11-22) database and a result-directed specific taxonomy database. The latter was a helpful hint to compare master protein kinds and reveal the insufficiency of specific venom proteomics characterization rules. Second, we suggested strict rules for protein identification to meet the requirements of forensic science on improved identification correctness, that is, (1) peptide spectrum matches confidence, peptide confidence, and protein confidence were both high (with the false-discovery ratio less than 1%); (2) the number of unique peptides was more than or equal to two in one protein, and (3) within unique peptides, which at least 75% of the ∆m/z of the matched y and b ions were less than 5 ppm. We identified these samples as cobra venom containing 10 highly abundant proteins (P00597, P82463, P60770, Q9YGI4, P62375, P49123, P80245, P60302, P01442, and P60304) from two snake venom protein families (acid phospholipase A2 and three-finger toxins), and the most abundant proteins were cytotoxins.