Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry

Human plasma is a readily available clinical sample that reflects the status of the body in normal physiological and disease states. Although the wide dynamic range and immense complexity of plasma proteins are obstacles, comprehensive proteomic analysis of human plasma is necessary for biomarker discovery and further verification. Various methods such as immunodepletion, protein equalization and hyper fractionation have been applied to reduce the influence of high-abundance proteins (HAPs) and to reduce the high level of complexity. However, the depth at which the human plasma proteome has been explored in a relatively short time frame has been limited, which impedes the transfer of proteomic techniques to clinical research. Development of an optimal strategy is expected to improve the efficiency of human plasma proteome profiling.     

Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

Precision proteomics requires high-resolution and high mass accuracy peptide measurements. The Orbitrap instrument achieves excellent resolution on a chromatographic time scale and its design is favorable for very high mass accuracy. Here we describe how mass precision for each peptide increases successively by considering all associated measurements, starting from the MS peak and proceeding to its chromatographic elution profile, isotope envelope, and stable isotope pair in SILAC measurements. We extract peptide charge pairs to perform nonlinear recalibration of the Orbitrap mass scale through spline interpolation. The deviation of mass values determined from charge pairs is used to convert mass precision to mass accuracy for subsequent database search. The corrected mass precision is consistent with the mass accuracy independently determined by database identification. Individual mass deviations range from below 100 ppb for peptides with many associated mass measurements and good signal intensities to low ppm for peptides with few mass measurements and signals close to the noise level. This extremely high and individualized mass accuracy is equivalent to a substantial increase in database identification score.     

Mass measurements of increased accuracy resolve heterogeneous populations of intact ribosomes

It is established that noncovalent complexes can be maintained both during and after electrospray and that assemblies of increasing size and complexity often lead to broadened peaks in mass spectra. This broadening arises from the tendency of large protein assemblies to form adducts with salts and is compounded when complexes are isolated directly from cells, without the full protein complement. To investigate the origins of this broadening in mass spectral peaks and to develop the optimal method for analyzing mass spectra of large protein complexes, we have carried out a systematic investigation of a series of noncovalent complexes representing a range of different sizes and architectures. We establish a positive correlation between peak width and the increased mass observed and show that this correlation is independent of the instrumental parameters employed. Using this relationship we show that we can determine masses of both 30S subunits and intact 2.3 MDa 70S ribosomes from Thermus thermophilus. The masses of both particles are consistent with multiple populations of ribosomes. To identify these various populations we combine simulated mass spectra of ribosomes, with and without the full protein complement, and estimate the extent of adducts from our study of known complexes. The results allow us to determine the contribution of the different subpopulations to the overall mass spectrum. We confirm the existence of these subpopulations using tandem mass spectrometry of intact 30S subunits. Overall, the results show that, rather than uniform particles, gas-phase ribosomes consist of a number of discrete populations. More generally, the results establish a rigorous procedure for accurate mass measurement and spectral analysis of heterogeneous macromolecular assemblies.     

Dynamics of ions of intact proteins in the Orbitrap mass analyzer

While allowing analysis of intact proteins without a theoretical upper mass limit, the Orbitrap mass analyzer demonstrates reduced resolving power as ion mass increases even at a constant mass-to-charge ratio. It is shown that this effect comes from the effects of ion scattering on background gas molecules. The main mechanisms causing decay of acquired transient appear to be fragmentation as well as accelerated dephasing of ion packets. Isotopic resolution of proteins including bovine serum albumin (MW 66.4 kDa) and transferrin (MW 78 kDa) has also been demonstrated. As a part of this study, detection of individual multiply-charged ions of myoglobin (MW 16.9 kDa) has been demonstrated. Quantized distribution of signal intensities for myoglobin ions well above the noise threshold was observed, with high mass accuracy and resolution of recorded individual ions used as an independent confirmation of correct assignment of signal to ions rather than to noise. The latter also allowed us to benchmark the sensitivity of image-current detection and explore in detail factors responsible for signal decay.     

Implementing Photodissociation in an Orbitrap Mass Spectrometer

We modified a dual pressure linear ion trap Orbitrap to permit infrared multiphoton dissociation (IRMPD) in the higher energy collisional dissociation (HCD) cell for high resolution analysis. A number of parameters, including the pressures of the C-trap and HCD cell, the radio frequency (rf) amplitude applied to the C-trap, and the HCD DC offset, were evaluated to optimize IRMPD efficiency and maintain a high signal-to-noise ratio. IRMPD was utilized for characterization of phosphopeptides, supercharged peptides, and N-terminal modified peptides, as well as for top-down protein analysis. The high resolution and high mass accuracy capabilities of the Orbitrap analyzer facilitated confident assignment of product ions arising from IRMPD.     

Validated hemoglobin-depletion approach for red blood cell lysate proteome analysis by means of 2D PAGE and Orbitrap MS

The analysis of the cytosolic red blood cell (RBC) proteome is negatively affected by the high intracellular amount of hemoglobin complicating the detection of low-abundant cytosolic proteins. In this study, an alternative approach for the preparation of hemoglobin-depleted RBC lysates is presented, which was established in combination with downstream 2D PAGE analysis and Orbitrap MS. Hemoglobin removal was accomplished by using HemoVoid(TM) depletion reagent, which enabled a very efficient enrichment of low-abundant proteins by simultaneously reducing the hemoglobin concentration of the sample. After defining selected sample preparation protocol characteristics including specificity/selectivity, precision and linearity, a 2D reference map (pH 4-7) of the cytosolic RBC proteome was generated and a total of 189 different proteins were identified. Thus, the presented approach proved to be highly suitable to prepare reproducible high-resolution 2D protein maps of the RBC cytosol and provides a helpful tool for future studies investigating disease- or storage-induced changes of the cytosolic RBC proteome.     

Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis

High-throughput DNA sequencing has resulted in increasing input in protein sequence databases. Today more than 20 genomes have been sequenced and many more will be completed in the near future, including the largest of them all, the human genome. Presently, sequence databases contain entries for more than 425.000 protein sequences. However, the cellular functions are determined by the set of proteins expressed in the cell – the proteome. Two-dimensional gel electrophoresis, mass spectrometry and bioinformatics have become important tools in correlating the proteome with the genome. The current dominant strategies for identification of proteins from gels based on peptide mass spectrometric fingerprinting and partial sequencing by mass spectrometry are described. After identification of the proteins the next challenge in proteome analysis is characterization of their post-translational modifications. The general problems associated with characterization of these directly from gel separated proteins are described and the current state of art for the determination of phosphorylation, glycosylation and proteolytic processing is illustrated. Received: 16 December 1999 / Accepted: 17 December 1999     

Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis

High-throughput DNA sequencing has resulted in increasing input in protein sequence databases. Today more than 20 genomes have been sequenced and many more will be completed in the near future, including the largest of them all, the human genome. Presently, sequence databases contain entries for more than 425.000 protein sequences. However, the cellular functions are determined by the set of proteins expressed in the cell--the proteome. Two-dimensional gel electrophoresis, mass spectrometry and bioinformatics have become important tools in correlating the proteome with the genome. The current dominant strategies for identification of proteins from gels based on peptide mass spectrometric fingerprinting and partial sequencing by mass spectrometry are described. After identification of the proteins the next challenge in proteome analysis is characterization of their post-translational modifications. The general problems associated with characterization of these directly from gel separated proteins are described and the current state of art for the determination of phosphorylation, glycosylation and proteolytic processing is illustrated.     

Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

Mass and top-down analyses of 150-kDa monoclonal immunoglobulin gamma (IgG) antibodies were performed on an Orbitrap analyzer. Three different sample delivery methods were tested including (1) infusion of an off-line desalted IgG sample using nano-electrospray; (2) on-line desalting followed by a step elution with a high percentage of organic solvent; and (3) reversed-phase HPLC separation and on-line mass and top-down analyses of disulfide isoforms of an IgG2 antibody. The accuracy of mass measurements of intact antibody was within ±2 Da (15 ppm). The glycoforms of intact IgG antibodies separated by 162 Da were baseline resolved. In-source fragmentation of the intact antibodies produced mainly 115 residue fragments including N-terminal variable domains of heavy and light chains. The sequence coverage (the number of cleavages) was greatly increased after reduction of disulfide bonds and HPLC/MS/MS analysis of light and heavy chains using collision-induced dissociation in the ion trap of the LTQ-Orbitrap. This is an attractive alternative to peptide mapping for characterization and monitoring of post-translational modifications attributed to minimal sample preparation, high speed of the mass/top-down analysis, and relatively minor method-induced sample modifications.     

超高效液相色谱-四极杆/静电场轨道阱高分辨质谱快速精准测定粮食中多种真菌毒素

采用直接提取稀释的快速前处理方法,结合稳定同位素稀释技术,利用超高效液相色谱-四极杆/静电场轨道阱高分辨质谱,建立了粮食中16种真菌毒素的快速精准分析方法。样品采用乙腈-水-乙酸溶液(70∶29∶1,体积比)提取,以C18色谱柱进行色谱分离,通过全扫描模式进行定量检测,并采用稳定同位素稀释以减少基质效应对定量分析的影响。结果表明,16种真菌毒素在一定浓度范围内均具有良好的线性关系,相关系数(r2)均大于0.999,4种常见粮食基质(小麦、玉米、大米、大麦)的限量浓度水平的加标回收率(n=6)为75.3%~123.5%,相对标准偏差为0.41%~14.7%。该方法简单、准确,适用于粮食中真菌毒素的检测,可满足日常监测工作的需要。     

Mass measurement accuracy comparisons between a double-focusing magnetic sector and a time-of-flight mass analyzer

We report a direct comparison of the mass measurement accuracies (MMAs) obtained on different mass spectrometry instrument types; a magnetic sector as the 'gold standard' and an electrospray ionization time-of-flight (ESI-TOF) instrument. Sixty samples, obtained from the Department of Chemistry at North Carolina State University, were analyzed on each instrument. Data are presented and compared between the different instruments. The average absolute MMAs achieved for the magnetic sector and Agilent ESI-TOF mass spectrometers were 3.0 and 1.1 ppm, respectively.     

Structural characterization of intact antibodies by high‐resolution LTQ Orbitrap mass spectrometry

Recombinant monoclonal antibodies (MAbs) can be heterogeneous due to modifications that can occur during expression, purification or during storage. These large multichain proteins (～150 kDa) are structurally challenging for detailed characterization to identify the sites of modifications. We report the use of LTQ Orbitrap mass spectrometry to accurately measure the average masses of individual glycoforms by direct infusion of an intact antibody. To identify the site‐specific modification of methionines in the antibody caused by forced oxidation, we used a ‘middle‐down’ approach. The antibody was subjected to limited digestion using the endoproteinase Lys‐C and reduced to generate Fab heavy chain, single chain Fc and light chain fragments (～25 kDa each). These species were subjected to on‐line liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) analysis using an LTQ Orbitrap, where these large precursors were dissociated by higher‐energy collisions in the C‐trap. High resolution and accuracy achieved for resulting fragments allowed us to show in a site‐specific manner that only the methionines in the Fc heavy chain were oxidized under the studied conditions. Copyright © 2009 John Wiley & Sons, Ltd.     

Automating proteome analysis: improvements in throughput, quality and accuracy of protein identification by peptide mass fingerprinting

The use of robots has major effects on maximizing the proteomic workflow required in an increasing number of high-throughput projects and on increasing the quality of the data. In peptide mass finger printing (PMF), automation of steps downstream of two-dimensional gel electrophoresis is essential. To achieve this goal, the workflow must be fluid. We have developed tools using macros written in Microsoft Excel and Word to complete the automation of our platform. Additionally, because sample preparation is crucial for identification of proteins by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, we optimized a sandwich method usable by any robot for spotting digests on a MALDI target. This procedure enables further efficient automated washing steps directly on the MALDI target. The success rate of PMF identification was evaluated for the automated sandwich method, and for the dried-droplet method implemented on the robot as recommended by the manufacturer. Of the two methods, the sandwich method achieved the highest identification success rate and sequence coverage of proteins.     

四极杆-轨道阱高分辨质谱联用技术用于食品中罂粟壳特征成份的确证

采用液相色谱-四极杆/轨道阱高分辨质谱(Q-Exactive)技术,建立了火锅底料、食品调味料、烤肉、凉皮中吗啡、可待因、蒂巴因、罂粟碱、那可丁5种生物碱的确证方法。样品在稀盐酸溶液中超声提取,经三氯甲烷除脂,离子交换固相萃取柱净化,氨化甲醇-乙酸乙酯洗脱,Accucore a Q色谱柱分离,电喷雾模式下通过静电场轨道阱全扫描得到5种生物碱的准分子离子峰,同时设定阈值自动触发二级质谱进行定性确证,同位素内标法定量,实现了食品中罂粟壳主要特征成份的筛查,同时对5种生物碱的特征子离子裂解方式进行研究。在最佳实验条件下,5种生物碱的质谱扫描质量精度误差小于5 ppm。吗啡的定量下限(LOQ)为2.0μg/kg,可待因为0.2μg/kg,罂粟碱、蒂巴因和那可丁为0.1μg/kg。分析物浓度与对应峰面积呈良好的线性关系(r20.999),方法回收率为63.4%~112.8%,相对标准偏差(RSD)为5.5%~13.6%。将该方法应用于多种实际样品分析,其定量结果准确,定性可靠。     

Qualitative Analysis of Multiple Phytochemical Compounds in Tojapride Based on UHPLC Q-Exactive Orbitrap Mass Spectrometry

Tojapride is composed of Caulis Perillae, Rhizoma Cyperi, Radix Glycyrrhizae, Citrus aurantium L., Coptis chinensis Franch, Pericarpium Citri Reticulatae, Reynoutria japonica Houtt, Tetradium ruticarpum, and Cleistocactus sepium. It has the effects of inhibiting gastric acid and relieving pain. It is clinically used for treating gastroesophageal reflux disease. To further study the pharmacodynamic properties of Tojapride, the systematic characterization of the chemical constituents in Tojapride was investigated using ultra-performance liquid chromatography with Q-Exactive Orbitrap mass spectrometry combined with parallel reaction monitoring for the first time. Eventually, a total of 222 compounds, including flavonoids, alkaloids, and glycyrrhizic acid derivatives, were identified based on the chromatographic retention times, MS/MS² information, and bibliography data; a total of 218 of these were reported for the first time as being present in Tojapride. This newly developed approach provides a powerful tool for extending our understanding of chemical constituents of Tojapride, which can be further extended to other TCMP composition research.     

液相色谱-四极杆/静电场轨道阱高分辨质谱鉴定一种新精神活性物质5F-MDMB-PICA在斑马鱼体内的代谢产物

通过建立斑马鱼模型研究5F-MDMB-PICA(3,3-二甲基-2-[1-(5-氟戊基)吲哚-3-甲酰氨基]丁酸甲酯)的体内代谢转化途径,利用液相色谱-四极杆/静电场轨道阱质谱(LC-Q-Orbitrap MS)技术,结合Mass Frontier软件对5F-MDMB-PICA及其代谢产物进行质谱解析和结构分析.结果表...     

Systematic Screening of Chemical Constituents in the Traditional Chinese Medicine Arnebiae Radix by UHPLC-Q-Exactive Orbitrap Mass Spectrometry

Arnebiae Radix (dried root of Arnebia euchroma (Royle) Johnst.) has been used in traditional Chinese medicine (TCM) to treat macular eruptions, measles, sore throat, carbuncles, burns, skin ulcers, and inflammation. Previous studies have shown that shikonins and shikonofurans are two of their main bioactive ingredients. However, systematic investigations of their constituents have rarely been conducted. It is necessary to establish a rapid and effective method to identify the chemical constituents of Arnebiae Radix. This will help to further improve the effective resource utilization rate of this plant. In this study, a rapid and effective UHPLC-Q-Exactive Orbitrap mass spectrometry method was established to simultaneously analyze chemical ingredients in Arnebiae Radix within a short period of time. Based on the results of a full scan MS, the MS² database (mzVault and mzCloud), the diagnostic fragment ions, the retention time, and the bibliography, a total of 188 compounds were identified, with 114 of those being reported from Arnebiae Radix for the first time. The results of this study lay the foundation for obtaining a thorough understanding of the active ingredients in Arnebiae Radix and its quality control. This method may be widely used for the chemical characterization of different samples.     

DART-Orbitrap质谱法对黄芩药材的快速分析

将实时直接分析(DART)离子源与高分辨率质谱Orbitrap联用,建立了一种对黄芩药材进行快速定性定量分析的方法。定性分析时,对其中的化学成分进行标准品比对和二级质谱确证,同时参考相应文献进行确认。定量分析时,采用Full MS-SIM及Targeted-MS2扫描方式采集信号,Targeted-MS2扫描方式下分别对黄芩素和汉黄芩素的母离子和子离子的提取离子流图积分,通过峰面积计算含量。在黄芩药材中检出黄芩素、汉黄芩素、韧黄芩素Ⅱ、二羟基-二甲氧基黄酮、5,7,2',5'-四羟基-8,6'-二甲氧基黄酮和SkullcapflavonⅡ的[M+H]+峰。定量分析结果显示,黄芩素(m/z 271.06→123.01)的线性范围为49.7~447.3 ng,相关系数(r2)为0.995,平均加标回收率为87.0%;汉黄芩素(m/z 285.07→270.05)的线性范围为50.0~350ng,r2为0.995,平均加标回收率为66.0%。该方法可用于黄芩药材的快速定性检测和定量分析。     

Improvement of proteome coverage using hydrophobic monolithic columns in shotgun proteome analysis

Monolithic columns are widely used in shotgun proteome analysis. However, it is difficult to increase the separation capability and proteome coverage by using conventionally organic polymer-based monolithic column due to the difficulty of controlling homogeneity of the overall pore structure (both pores and microglobules), which leads to relatively low column efficiency. Therefore, we studied the effect of constitute and percentage of porogenic solvent, functional monomer, column length, and separation gradient on the peak capacity and proteome coverage by methacrylate-based reversed phase monolithic columns. It was demonstrated that the porous property of the hydrophobic monolith, which was mainly determined by the porogenic solvent, was crucial to the proteome coverage when similar methacrylate monomer was utilized and a ternary porogenic solvent was adopted to prepare C12 monolithic column with relatively homogeneous overall pore structure. It was also shown that high proteome coverage could be reliably obtained with online multidimensional separation using totally monolithic columns system with the length of analytical column at 85 cm and reversed phase separation gradient at 210 min.