MALDI‐TOF Mass‐Spectrometry‐Based Versatile Method for the Characterization of Protein Kinases

We describe a MALDI‐TOF mass‐spectrometry‐based method that is rapid and versatile for the characterization of protein kinases and their inhibitors. We have designed new kinase substrates by the modification of common synthetic peptides, such as kemptide (LRRALS G), CaMKII substrate (KRQQS FDLF), erktide (ATGPLS PGPFGRR), abltide (EAIY AAPFAKKK), srctide (AEEEIY GEFEAKKKK), neurogranin (AAAKIQAS FRGHMARKK), and casein kinase I (CKI) substrate (RRKDLHDDEEDEAMS ITA). There are two fundamental points on which the proposed method is based to improve the mass‐spectrometric response: 1) mass tag technology by N‐derivatization through stable isotope labeling and 2) C‐terminal conjugation with tryptophanylarginine (WR). It was suggested that C‐terminal conjugation with the WR moiety enhances the ionization potency of these new substrates 1.5–13.7 times as much as those of the original peptides. We demonstrated, by using modified abltide (Ac‐EAIY AAPFAKKKWR‐NH₂), that WR conjugation at the C‐terminus in combination with stable‐isotope labeling at the N‐terminus allowed the quantitative assay of recombinant c‐Abl kinase in the presence of adenosine 5′‐triphosphate (ATP; K_M,ATP=18.6 μM and V_max=642 pmol min^?1 μg^?1). The present protocol made a simple and reliable inhibition assay of recombinant c‐Abl kinase by imatinib possible (IC_{50(recombinant)}=291 nM ; STI571, Gleevec; Novartis Pharma). Moreover, it was also demonstrated that this ATP noncompetitive inhibitor differentiates between two conformers of c‐Abl kinases: the phosphorylated active and dephosphorylated inactive forms (IC_{50(active form)}=1049 nM and IC_{50(inactive form)}=54 nM ). The merit of this approach is evident because the present protocol can be applied to the direct monitoring of the activities of living cell kinases by using cancer‐cell lines, such as mouse B16 melanoma cells and human lung cancer K562 cells. A multiple‐kinase assay that uses K562 cell lysate in the presence of seven new synthetic substrates made high‐throughput inhibitor profiling possible. It should be emphasized that this radioactive isotope‐free quantitative kinase assay will greatly accelerate the discovery of a new generation of potential kinase inhibitors that exhibit highly selective or unique inhibitory profiles.     

A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins

Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non‐specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid‐binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent‐resistant lipids bound at the dimer interface in the leucine transporter show decreased k_off rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid‐II results in the formation of a 1:1 protein–lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non‐annular lipids based on their exchange rates in solution.     

Mass‐spectrometry‐based lipidomics

Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large‐scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass‐spectrometry‐based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass‐spectrometry‐based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass‐spectrometry‐based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single‐cell lipidomics, flux‐based lipidomics and multiomics technologies were also reviewed.     

Ultraviolet Photodissociation Induced by Light‐Emitting Diodes in a Planar Ion Trap

The first application of light‐emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.     

Chip‐Based Free‐Flow Electrophoresis with Integrated Nanospray Mass‐Spectrometry

Free‐flow electrophoresis is an ideal tool for preparative separations in continuous microflow. With the approach presented herein for coupling free‐flow electrophoresis and mass spectrometry it is now also possible to trace non‐fluorescent compounds and identify them by means of mass spectrometry. The functionality of the method and its potential as an integrated separation unit for microflow synthesis is demonstrated by application to a multicomponent [3+2]‐cycloannulation.     

Laser‐Initiated Radical Trifluoromethylation of Peptides and Proteins: Application to Mass‐Spectrometry‐Based Protein Footprinting

Described is a novel, laser‐initiated radical trifluoromethylation for protein footprinting and its broad residue coverage. ^.CF₃ reacts with 18 of the 20 common amino acids, including Gly, Ala, Ser, Thr, Asp, and Glu, which are relatively silent with regard to ^.OH. This new approach to footprinting is a bridge between trifluoromethylation in materials and medicinal chemistry and structural biology and biotechnology. Its application to a membrane protein and to myoglobin show that the approach is sensitive to protein conformational change and solvent accessibility.     

Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free‐Electron Laser Pulses

The fragmentation of free tenfold protonated ubiquitin in intense 70 femtosecond pulses of 90 eV photons from the FLASH facility was investigated. Mass spectrometric investigation of the fragment cations produced after removal of many electrons revealed fragmentation predominantly into immonium ions and related ions, with yields increasing linearly with intensity. Ionization clearly triggers a localized molecular response that occurs before the excitation energy equilibrates. Consistent with this interpretation, the effect is almost unaffected by the charge state, as fragmentation of sixfold deprotonated ubiquitin leads to a very similar fragmentation pattern. Ubiquitin responds to EUV multiphoton ionization as an ensemble of small peptides.     

Photodissociation Spectroscopy of CD3I+ Generated by Mass‐Analyzed Threshold Ionization for Structure Determination

A method is devised better to resolve the subbands of the ground vibronic band in the mass‐analyzed threshold ionization (MATI) spectrum of CD₃I. By selective photodissociation of CD₃I⁺ in these subbands, high‐resolution spectra for the à ²A₁← ²E_3/2 transition are recorded. Spectral analysis confirms our previous suggestion that these subbands are due to cations in different rotational K states; this demonstrates the capability of MATI to generate rovibronically selected ion beams. By using the rotational constants of CH₃I⁺ and CD₃I⁺ obtained by spectral analysis, the zero‐point‐level geometries of the cations in the ²E_3/2 and à ²A₁ states are determined. To the best of our knowledge, this is the first time that the capability of MATI–PD to determine the geometry of a gas‐phase polyatomic cation in an excited electronic state is demonstrated.     

Applications of solid‐phase micro‐extraction with mass spectrometry in pesticide analysis

Pesticides, widely applied in agriculture, can produce a variety of transformation products and their continuous use causes deleterious effects to ecosystem. Efficient and sensitive analytical techniques for enrichment and analysis of pesticides samples are highly required. Compared with other extraction methods, solid‐phase micro extraction is a solvent free, cost effective, robust, versatile, and high throughput sample preparation technique, especially for the analysis of pesticides from complicated matrices. Coupling of solid‐phase micro extraction with gas chromatography and mass spectrometry and liquid chromatography–mass spectrometry has been extensively applied in pesticide analysis. On the other hand, in recent years, combination of fast separation using solid‐phase micro extraction and rapid detection using ambient mass spectrometry is providing highly efficient pesticide screening. This article summarizes the applications of solid‐phase micro extraction coupled to mass spectrometry for pesticides analysis.     

High‐Throughput Proteomics Enabled by a Photocleavable Surfactant

Mass spectrometry (MS)‐based proteomics provides unprecedented opportunities for understanding the structure and function of proteins in complex biological systems; however, protein solubility and sample preparation before MS remain a bottleneck preventing high‐throughput proteomics. Herein, we report a high‐throughput bottom‐up proteomic method enabled by a newly developed MS‐compatible photocleavable surfactant, 4‐hexylphenylazosulfonate (Azo) that facilitates robust protein extraction, rapid enzymatic digestion (30 min compared to overnight), and subsequent MS‐analysis following UV degradation. Moreover, we developed an Azo‐aided bottom‐up method for analysis of integral membrane proteins, which are key drug targets and are generally underrepresented in global proteomic studies. Furthermore, we demonstrated the ability of Azo to serve as an “all‐in‐one” MS‐compatible surfactant for both top‐down and bottom‐up proteomics, with streamlined workflows for high‐throughput proteomics amenable to clinical applications.     

Mass‐spectrometry‐directed analysis and purification of pyrrolizidine alkaloid cis/trans isomers in Gynura japonica

Pyrrolizidine alkaloids are highly hepatotoxic natural chemicals that produce irreversible chronic and acute hepatotoxic effects on human beings. Purification of large amounts of pyrrolizidine alkaloids is necessary for toxicity studies. In this study, an efficient method for targeted analysis and purification of pyrrolizidine alkaloid cis/trans isomers from herbal materials was developed for the first time. Targeted analysis of the hepatotoxic pyrrolizidine alkaloids was performed by liquid chromatography with tandem mass spectrometry (precursor ion scan and daughter ion scan), and the purification of pyrrolizidine alkaloids was achieved with a mass‐directed auto purification system. The extraction and preparative liquid chromatography conditions were optimized. The developed method was applied to analysis of Gynura japonica (Thunb.) Juel., a herbal medicine traditionally used for detumescence and relieving pain but is potentially hepatotoxic as it contains pyrrolizidine alkaloids. Twelve pyrrolizidine alkaloids (six cis/trans isomer pairs) were identified with reference compounds or characterized by liquid chromatography with tandem mass spectrometry, and five individual pyrrolizidine alkaloids, including (E)‐seneciphylline, seneciphylline, integerrimine, senecionine, and seneciphyllinine, were prepared from G. japonica roots with high efficiency. The results of this work provide a new technique for the preparation of large amounts of pyrrolizidine alkaloid reference substances, which will also benefit toxicological studies of pyrrolizidine alkaloids and treatments for pyrrolizidine alkaloid‐induced toxicity.     

应用非同质荷比规则提高蛋白质组学检索结果的可信度和灵敏度

如何筛选合理的数据库匹配结果对于基于质谱的蛋白质组学研究至关重要。但是目前,基于打分体系和反转数据库的筛选方法都无法有效的避免假阳性和假阴性匹配的存在。因此,本文提出了一种系统的搜索策略: 非同质荷比检索规则 (INMZS)。在该策略中,所有匹配结果都需要检查相关匹配质荷比的分享程度,只有那些相关质荷比均为专有匹配时,蛋白质才会被作为可信结果保留,策略还采用迭代搜索方法以提高鉴定低丰度组分的灵敏度。最终,所有的匹配结果由诱饵数据库方法进行评估以得到最终结果列表。INMZS策略在标准蛋白质混合物和大规模人肝蛋白质组数据上进行了模拟及应用,结果显示,INMZS规则和诱饵数据库评估方法的结和可以有效的保证蛋白质组学数据匹配的可信度及灵敏度,可以广泛适用于基于二维凝胶电泳及非shotgun技术的蛋白组学研究中。     

Mass‐Selected Circular Dichroism of Supersonic‐Beam‐Cooled [D4]‐(R)‐(+)‐3‐Methylcyclopentanone

UV spectroscopy and electronic circular dichroism (ECD) experiments on supersonic‐beam‐cooled deuterated (R)‐(+)‐3‐methylcyclopentanone ([D₄]‐(R)‐(+)‐3‐MCP) have been performed by using a laser mass spectrometer. The spectral resolution not only allowed excitation and CD measurements for single vibronic transitions but also for the rotational P, Q, and R branches of these transitions. The investigated transition showed the largest anisotropy factor ever observed for chiral molecules in the gas phase, which, due to residual saturation of the excited transition, represents only a lower limit for the real anisotropy factor. Furthermore, one‐color (1+1+1) and two‐color (1+1′) resonance‐enhanced multiphoton ionization (REMPI) measurements were performed and the effusive‐beam (room temperature) and supersonic‐beam results for [D₄]‐(R)‐(+)‐3‐MCP were compared. These results allowed a differentiation between single‐step ECD (comparable to conventional ECD) and cumulative ECD (only possible in multiphoton excitation) under supersonic‐beam conditions.     

Electron‐Transfer Kinetics of Microperoxidase‐11 Covalently Immobilised onto the Surface of Multi‐Walled Carbon Nanotubes by Reactive Landing of Mass‐Selected Ions

Controlled deposition of biological molecules on nanostructured materials is a basic step towards the realisation of biochip components. In this study we report the investigation of the first covalent immobilisation of mass‐selected redox protein on a carboxyl‐functionalised multi‐walled carbon nanotube (MWCNT) electrode surface by means of ion soft landing. The immobilised protein maintains its biochemical properties, displaying an excellent electrochemical behaviour on the electrode surface. The deposition of mass‐selected ions is influenced by several factors, including the charge state and the collision energy of the projectile ions. To elucidate the mechanism involved in the protein reactive landing onto the MWCNT surface, the data obtained from cyclic voltammetry experiments were modelled according to the Marcus theory. The proposed method opens up the way to the development of a new generation of biocomponents with potential use in biosensors, diagnostics, biofuel cells and bioactive films.     

‘Extreme Mass Spectrometry’: the role of mass spectrometry in the study of the Antarctic Environment

A focus on the studies of the Antarctic environment that have been performed by mass spectrometry is presented herein; our aim is to give evidence of the essential role of this instrumental technique in the framework of the scientific research in Antarctica, with a comprehensive review on the main literature of the last two decades. Due to the wideness of the topic, the present review is limited to the determination of organic pollutants, natural molecules and biomarkers in Antarctica, thus excluding elemental analysis and studies on inorganic species. The work has been divided into five sections, on the basis of the considered environmental compartment: air; ice and snow; seawater, pack ice and lakes; soil and sediments; and organisms and biomarkers. Copyright © 2014 John Wiley & Sons, Ltd.     

Analysis of Cembranoids in Flue‐cured Tobacco by Accelerated Solvent Extraction and Gas Chromatography‐Mass Spectrometry‐Selected Ion Monitoring

An efficient and sensitive analytical method based on accelerated solvent extraction (ASE) and gas chromatography‐mass spectrometry‐selected ion monitoring (GC‐MS‐SIM) was developed and validated for analysis of cembranoids in flue‐cured tobacco leaves. Extraction efficiency of different pretreatment methods including liquid‐solid extraction (LSE), ultrasound‐assisted extraction (UAE), Soxlet extraction and accelerated solvent extraction (ASE) was compared and ASE was chosen as the optimal extraction method. During ASE procedure, effect of four parameters on extraction efficiency was considered and the experimental conditions were selected as follows: extraction solvent: dichloromethane; oven temperature: 50 °C; static time: 5 min and number of cycles: 2. Working standards of cembranoids were isolated by silica gel column chromatography and the identification was performed by mass spectrometry. Performance characteristics such as linearity, limit of detection (LOD), limit of quantitation (LOQ), precision and recovery were studied. The LOD and LOQ values were ranging from 5.0 × 10^?3 to 6.9 × 10^?3 μg/mL and 1.7 × 10^?2 to 2.3 × 10^?2 μg/mL for all analytes. At three different spiked levels, recoveries for CBT‐ol, α‐CBT‐diol and β‐CBT‐diol were 94.6%‐105.1%, 93.0%‐97.2% and 88.7%‐107.5% while the relative standard deviations (RSDs) were in the ranges of 3.9%‐6.2%, 1.8%‐8.7% and 1.7%‐6.0%, respectively. The proposed analytical methodology was successfully applied in the analysis of cembranoids in tobacco samples.