Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry

We have developed a method for the rapid and unambiguous identification of sequences of hit compounds from one-bead-one-compound combinatorial libraries of peptide and peptoid ligands. The approach uses a cleavable linker that is hydrophilic to help reduce nonspecific binding to biological samples and allows for the attachment of a halogen tag, which greatly facilitates post-screening sequencing by tandem mass spectrometry (MS/MS). The linker is based on a tartaric acid unit, which, upon cleavage from resin, generates a C-terminal aldehyde. This aldehyde can then be derivatized with a bromine-containing amino-oxy compound that serves as an isotope tag for subsequent MS/MS analysis of y-ion fragments. We have applied this linker and method to the syntheses of a number of peptoids that vary in sequence and length and have also demonstrated single-bead sequencing of a peptoid pentamer. The linker is also shown to have very low levels of nonspecific binding to proteins.     

New applications of multiply charged ionic probes as cleavable cross-linker and polymerization reagent

We have designed new cleavable cross-linkers for biomolecules containing the 2,6-bis(oxazolinyl)pyridine (pybox) lanthanum complex. These species can effectively donate multiple charges to afford cross-linker ions for target biomolecules. The cross-linkers are cleaved easily by adding water. Moreover, we were able to detect chain structures of target molecules, including biomolecules and carbon clusters, such as fullerene C₆₀, by the addition of some MS ionic probes. Cold-spray ionization mass spectrometry demonstrated the applications of multiply charged ionic probes as cleavable cross-linkers and polymerization reagents.     

Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition

The azide-alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide-alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na(2)S(2)O(4), 2% HOCH(2)CH(2)SH, 10% HCO(2)H, 95% CF(3)CO(2)H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO(2)H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies.     

Characterization of tetrathiofulvalene compounds using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Tetrathiofulvalene compounds are important components of charge-transfer complexes, which may be applied in various fields of scientific research and practical applications. Some of these compounds cannot be characterized by mass spectrometry. Here, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry was used for the characterization of tetrathiofulvalenes. The samples could be easily desorbed and ionized to form singly charged ions, and mass spectra with isotopic resolution readily obtained. The mass spectrometric results for 26 compounds have shown that MALDI-TOF is more effective and convenient than other mass spectrometry methods, and resolves the problem of mass spectrometric characterization of tetrathiofulvalene compounds.     

Gas Chromatography‐Mass Spectrometry‐Basic Principles,Instrumentation and Selected Applications for Detection of Organic Compounds

Abstract

This mini‐review discusses the analytical technique of gas chromatography‐mass spectrometry (GC‐MS), specifically basic principles and instrumentations. The applications of GC‐MS to a number of studies for determining organic compounds from around the world are presented and highlight its universal use and acceptance. Selected applications show that GC‐MS is an integral and complimentary part of many field studies involving organic compound detection and determination.     

Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics

The advances in bioorthogonal ligation methods have provided new opportunities for proteomic analysis of newly synthesized proteins, posttranslational modifications, and specific enzyme families using azide/alkyne-functionalized chemical reporters and activity-based probes. Efficient enrichment and elution of azide/alkyne-labeled proteins with selectively cleavable affinity tags are essential for protein identification and quantification applications. Here, we report the synthesis and comparative analysis of Na?S?O?-cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. We demonstrated that ortho-hydroxyl substituent is required for efficient azobenzene-bond cleavage and show that these cleavable affinity tags can be used to identify newly synthesized proteins in bacteria targeted by amino acid chemical reporters as well as their sites of modification on endogenously expressed proteins. The azobenzene-based affinity tags are compatible with in-gel, in-solution, and on-bead enrichment strategies and should afford useful tools for diverse bioorthogonal proteomic applications.     

Analysis of drugs, natural and bioactive compounds containing phenolic groups by capillary electrophoresis coupled to mass spectrometry

This review summarizes the use of capillary electrophoresis (CE) coupled to mass spectrometry (MS) for the analysis of phenolic compounds and its latest developments. Special attention is paid to the different interfaces. The instrumental setups are discussed and demonstrated in a high number of real applications.     

气相色谱-质谱法分析硫芥子气及相关化合物

用气相色谱－质谱法对含硫芥子气类化合物进行了分析。探讨了长链芥子气的电子轰击电离的质谱规律，并对待测化合物的色谱保留数据进行了研究，在给定条件下，各种待测含硫芥子气在气相色谱柱中能有效的分离和鉴定。     

Synthesis and cleavage of core‐labile poly(alkyl methacrylate) star polymers

Core‐cleavable star polymers were synthesized by the coupling of living anionic poly(alkyl methacrylate) arms with either dicumyl alcohol dimethacrylate (DCDMA) or 2,5‐dimethyl‐2,5‐hexanediol dimethacrylate (DHDMA). This synthetic methodology led to the formation of star polymers that exhibited high molecular weights and relatively narrow molecular weight distributions. The labile tertiary alkyl esters in the DCDMA and DHDMA star polymer cores were readily hydrolyzed under acidic conditions. High‐molecular‐weight star polymer cleavage led to well‐defined arm polymers with lower molecular weights. Hydrolysis was confirmed via ¹H NMR spectroscopy and gel permeation chromatography. Thermogravimetric analysis (TGA) of the star polymers demonstrated that the DCDMA and DHDMA star polymer cores also thermally degraded in the absence of acid catalysts at 185 and 220 °C, respectively, and the core‐cleavage temperatures were independent of the arm polymer composition. The difference in the core‐degradation temperatures was attributed to the increased reactivity of the DCDMA‐derived cores. TGA/mass spectrometry detected the evolution of the diene byproduct of the core degradation and confirmed the proposed degradation mechanism. The DCDMA monomer exhibited a higher degradation rate than DHDMA under identical reaction conditions because of the additional resonance stabilization of the liberated byproduct, which made it a more responsive cleavable coupling monomer than DHDMA. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3083–3093, 2003     

An investigation of dipeptides containing polar and nonpolar side groups by curie-point pyrolysis tandem mass spectrometry

Methionyl-leucine, leucyl-methionine, phenylalanyl-leucine, and leucyl-phenylalanine have been analyzed to determine dipeptide fragmentation mechanisms in Curie-point pyrolysis tandem mass spectrometry. Results show that fragmentations of dipeptides follow two general pathways, one involving direct cleavage of the dipeptide and the other involving cyclization of the dipeptide. Unique products and strong changes in relative mass spectral peak intensities arise, depending on constituent amino acid residues and their sequence. Also, the length and nature of the side groups strongly direct fragmentation. From these results, the major peaks in the spectra of eight other dipeptides could be readily explained; this suggests that a significant number of dipeptides follow the same general fragmentation mechanisms.     

Structural characterization of monohydroxyeicosatetraenoic acids and dihydroxy- and trihydroxyeicosatrienoic acids by ESI-FTICR

The fragmentation characteristics of monohydroxyeicosatetraenoic acids and dihydroxy- and trihydroxyeicosatrienoic acids were investigated by electrospray ionization Fourier transform ion cyclotron resonance (FTICR) mass spectrometry using sustained off-resonance irradiation collision-induced dissociation (SORI-CID) and infrared multiphoton dissociation (IRMPD). The fragmentation patterns of these compounds were associated with the number and positions of the hydroxyl substituents. The fragmentation is more complicated with increasing number of the hydroxyl groups of the compounds. In general, the major carbon-carbon cleavage of [M−H]⁻ ions occurred at the α-position to the hydroxyl group, and the carbon-carbon cleavage occurred when there was a double-bond at the β-position to the hydroxyl group. SORI-CID and IRMPD produced some common fragmentation patterns; however, each technique provided some unique patterns that are useful for structural identification of these compounds. This study demonstrated the application of FTICR via the identification of regioisomers of trihydroxyeicosatrienoic acids in rabbit aorta samples.     

Matrix-assisted laser desorption/ionization mass spectrometry of taxanes

Taxanes are biologically active compounds that have been extensively used in pharmacology for their powerful anticancer properties. High specificity and low level sensitivity for analysis of these compounds have been obtained with reversed-phase high-pressure liquid chromatography/mass spectrometry (RP-HPLC/MS), but the number of applications of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for low molecular weight analytes is rapidly growing. A new MALDI-MS approach for the rapid screening of a variety of taxanes and a tandem mass spectrometric (MS/MS) analysis of the most important and diagnostic taxane fragmentation pathways are proposed. A solid-phase extraction method followed by preliminary quantification is also reported.     

Structural characterization of steroidal saponins by electrospray ionization and fast-atom bombardment tandem mass spectrometry

The structural characterization of four steroidal saponin compounds involving two and three sugar groups, namely spirostanol saponins and furostanol saponins, were investigated by positive ion fast-atom bombardment (FAB), electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) techniques. Important structural information was obtained from collision-induced dissociation (CID) and FAB-MS spectra with different liquid matrices. It was found that a characteristic fragmentation involving the loss of 144 Da arising from the cleavage of the E-ring was observed when there was no sugar chain at the C-26 position. When a glucoside group was substituted at the C-26 position, this C-26 sugar moiety was preferentially eliminated. All of these compounds produced a major product ion with a stable skeleton structure at m/z 255. The results of this paper can assist structural analysis of mixtures of steroidal saponins.     

Highly Multiplexed Single‐Cell In Situ Protein Analysis with Cleavable Fluorescent Antibodies

Limitations on the number of proteins that can be quantified in single cells in situ impede advances in our deep understanding of normal cell physiology and disease pathogenesis. Herein, we present a highly multiplexed single‐cell in situ protein analysis approach that is based on chemically cleavable fluorescent antibodies. In this method, antibodies tethered to fluorophores through a novel azide‐based cleavable linker are utilized to detect their protein targets. After fluorescence imaging and data storage, the fluorophores coupled to the antibodies are efficiently cleaved without loss of protein target antigenicity. Upon continuous cycles of target recognition, fluorescence imaging, and fluorophore cleavage, this approach has the potential to quantify over 100 different proteins in individual cells at optical resolution. This single‐cell in situ protein profiling technology will have wide applications in signaling network analysis, molecular diagnosis, and cellular targeted therapies.     

A novel and rapid encoding method based on mass spectrometry for "one-bead-one-compound" small molecule combinatorial libraries

A novel and efficient encoding method based on mass spectrometry for "one-bead-one-compound" small molecule combinatorial libraries has been developed. The topologically segregated bifunctional resin beads with orthogonal protecting groups in the outer and inner regions are first prepared according to our previously published procedure. Prior to library synthesis, the inner core of each bead is derivatized with 3-4 different coding blocks on a cleavable linker. Each functional group on the scaffold is encoded by an individual coding block containing a functional group with the same chemical reactivity. During the library synthesis, the same chemical reactions take place on the scaffold (outer layer of the bead) and coding blocks (inner core of the bead) concurrently. After screening, the coding tags in the positive beads are released, followed by molecular mass determination using matrix-assisted laser desorption ionization Fourier transform mass spectrometry. The chemical structure of library compounds can be readily identified according to the molecular masses of the coding tags. The feasibility and efficiency of this approach were demonstrated by the synthesis and screening of a model small molecule library containing 84 672 member compounds, with a model receptor, streptavidin. Streptavidin binding ligands with structural similarity (17) were identified. The decoding results were clear and unambiguous.     

复方板蓝根颗粒化学成分的质谱研究

利用电喷雾多级串联质谱(ESI-MSn)和傅里叶变换离子回旋共振质谱(FT-ICR-MS)技术,对复方板蓝根颗粒经溶剂萃取后的95%(体积分数)醇提和水提部位的化学成分进行了系统研究,鉴定出多种氨基酸成分、糖及其衍生物、有机酸、氨基酸和单糖的梅拉德反应初级产物以及含硫化合物表告依春.该方法灵敏快速,适宜于中药提取物的化学成分分析.     

Identification of components in waste streams by electrospray and tandem mass spectrometry

Highly polar, non-gas-chromatographable compounds have few unambiguous analysis protocols for environmental applications. A recent environmental investigation, concerning the identification of a non-gas-chromatographable yellow component in chemical waste water and in effluents from a biological wastewater treatment plant required the use of a number of analytical approaches. Electrospray mass spectrometry, tandem mass spectrometry, high-performance liquid chromatography, nuclear magnetic resonance, and molecular spectroscopy of commercial and synthesized chlorodinitrophenol isomers were required in order to identify the specific isomer causing the color. The present report summarizes the electrospray ionization and tandem mass spectrometric studies that were used. The mass spectrometric study shows that two different isomers of chlorodinitrophenol exhibit very different collision-induced dissociation (CID) spectra. Differences in the tandem mass spectra can be attributed to the different structures of the anions formed from these two different isomers. Instrumentation that uses electrospray ionization and produces CID mass spectra and optical absorption spectra in a single analysis may be required in order to produce highly specific information on non-gas-chromatographable compounds found in the environment.     

Fragmentation pathways of oxygenated tetracyclic triterpenoids and their application in the qualitative analysis of Ganoderma lucidum by multistage tandem mass spectrometry

The fragmentation pathways of oxygenated tetracyclic triterpenoids from Ganoderma lucidum were systematically studied based on interpreting the mass spectra of 44 known triterpenoids using a combination of multistage tandem mass spectrometry (MS(n)) experiments and high-resolution mass spectrometry (HRMS) analysis. In negative ion mode, the fragmentation pathways of triterpenoid acids are rather characteristic. After the prominent loss of H(2) O or CO(2), cleavages take place on the A, B, C and D rings. Interestingly, the cleavage mode is highly dependent on the positions of the carbonyl groups and hydroxyl groups in the tetracyclic skeleton. Characteristic cleavage of ring A occurs in 7-oxo-11-H or 7-oxo-11-hydroxy derivatives; characteristic cleavage of ring B occurs in the 7-oxo-11-hydroxy derivatives; characteristic cleavage of ring C occurs in the 7-hydroxy-15-oxo derivatives; while the cleavage of ring D can be observed in the majority of the compounds investigated. The odd-electron species, which disobey the 'even-electron rule', are also observed and discussed in this paper. These phenomena provide an easy way to determine the tetracyclic skeleton and distinguish the isomers of the triterpenoids from each other. What is more, the fragmentation pathways of triterpenoid alcohols were also investigated in positive ion mode. The accurate masses of the product ions were determined using quadrupole orthogonal time-of-flight (QTOF) instruments. Finally, the fragmentation rules were applied to identify the components of G. lucidum. As a result, 73 triterpenoids including 11 new ones were identified. The triterpenoids were classified into six subclasses according to their different fragmentation behaviors. The application of tandem mass spectrometry was further explored.     

超高效液相色谱-四极杆-飞行时间质谱定性研究茶叶籽中的酚类化合物

采用超高效液相色谱(UHPLC)-四极杆-飞行时间质谱(Q-TOF/MS)技术定性分析茶叶籽中的酚类化合物。茶叶籽样品经乙醇水溶液提取后经反相色谱分离,通过Q-TOF/MS进行化合物的鉴定。基于山茶属及相关植物化学组成的文献,建立了一个含有106种酚类化合物的数据库。对UHPLC-Q-TOF/MS采集得到的一级质谱数据进行数据库检索,然后对检索到的化合物色谱峰进行二级质谱扫描,根据得到的碎片离子推断化合物的结构。初步推断出茶叶籽提取物中的24种酚类化合物,包括13种酚酸类、4种儿茶素类和7种黄酮类化合物,并通过与标准品比对,进一步确证了这些化合物。结果表明UHPLC-Q-TOF/MS技术可以用于对茶叶籽中酚类化合物进行快速、准确、可靠的定性分析,促进新化合物的发现与鉴别。     

Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors

Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.