Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry

A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain.     

Dissociation behavior of a bifunctional tempo‐active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry

We have synthesized a homobifunctional active ester cross‐linking reagent containing a TEMPO (2,2,6,6‐tetramethylpiperidine‐1‐oxy) moiety connected to a benzyl group (Bz), termed TEMPO‐Bz‐linker. The aim for designing this novel cross‐linker was to facilitate MS analysis of cross‐linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO‐Bz‐linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof‐of‐principle study was to evaluate the potential of the TEMPO‐Bz‐linker for chemical cross‐linking studies to derive 3D‐structure information of proteins. Our studies were motivated by the well documented instability of the central NO―C bond of TEMPO‐Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO―C bond of the TEMPO‐Bz‐linker. This leads to the formation of complementary open‐shell peptide radical cations, while precursor ions that are protonated at the TEMPO‐Bz‐linker itself exhibit a charge‐driven formation of even‐electron product ions upon collision activation. MS³ product ion experiments provided amino acid sequence information and allowed determining the cross‐linking site. Our study fully characterizes the CID behavior of the TEMPO‐Bz‐linker and demonstrates its potential, but also its limitations for chemical cross‐linking applications utilizing the special features of open‐shell peptide ions on the basis of selective tandem MS analysis. Copyright © 2015 John Wiley & Sons, Ltd.     

HRGC and GC–MS analysis of essential oil from colombian ylang-ylang (Cananga odorata Hook fil. et Thomson,forma genuina)

Samples of essential oil from Colombian ylang-ylang trees were analyzed by means of HRGC, HRGC–MS, IR and ¹H- and ¹³C-NMR. 57 components were detected, 51 of which were positively identified. Camphene and anethol were identified in ylang-ylang essential oil for the first time. Among the composition-determining variables studied (extraction time, part of the flower, and flower freshness), the extraction time and the flower condition (fresh versus dry) were found to have the largest incidence in the quality of the essential oil.     

Quantitative performance of liquid chromatography coupled to Q-Exactive high resolution mass spectrometry (HRMS) for the analysis of tetracyclines in a complex matrix

The presence of antibiotics in the environment is of increased interest and, as modern mass spectrometers become more efficient, we are increasingly aware of traces of pharmaceuticals appearing in a wide range of environmental and biological matrices. The Q-Exactive mass spectrometer is part of these innovative hybrid high-resolution mass spectrometers (HRMS) which is often associated with peptide sequencing or metabolomics but with a limited number of studies focusing on its application to the quantification of small molecules in environmental and biological matrices. It combines the high resolving power (RP) performance of the Orbitrap with the high performance selectivity of the quadrupole. Tetracyclines (TCs) are a family comprising some of the most widely used antibiotics in veterinary medicine. This study presents the quantitative performances of the Q-Exactive by illustrating a new approach to quantify TCs using liquid chromatography coupled to a HRMS in a complex matrix, i.e., swine manure. The Q-Exactive was used at high-resolution in both full scan (FS) and targeted ion fragmentation (tMS²) modes. These two modes were optimized and compared to determine the most reliable and efficient approach to quantify TCs with good accuracy. The proposed method was optimized to obtain the best selectivity and sensitivity, thus eliminating false positive and allowing the detection of trace levels of analyte. The TCs were extracted from the matrix by sonication using McIlvaine buffer followed by an off-line solid phase extraction method to concentrate and clean the extracts. Both FS and tMS² modes presented good linearity (R² > 0.991) and repeatability (RSD < 15%). Mass accuracy was acceptable with values below 2 ppm. The method detection limits (MLD) calculated from the calibration curves ranged from 2.0 to 12 ng g⁻¹ for FS mode and from 1.5 to 3.6 ng g⁻¹ for tMS² mode. Accuracy and interday/intraday relative standard deviations were below 21% for both modes studied. TCs were quantified in real samples of swine manure with concentrations ranging from 29 to 75 ng g⁻¹. This study showed the possibility of using hybrid HRMS for trace detection and quantification of TCs in a complex matrix, thus avoiding false positive while achieving good selectivity and sensitivity.     

The use of multidimensional capillary chromatography in conjunction with a triple quadropule mass-spectrometer in the analysis of complex mixtures (GC-GC-MS-MS)

The analysis of complex mixtures, such as essential oils requires high resolution chromatographic separation and even the use of very efficient columns cannot prevent the overlapping of certain peaks. This means that it is very difficult to obtain high quality mass spectra when the sample contains numerous constituants. The pre-separation by column or preparative GC leads to a considerable loss of material and, often, to the formation of artefacts. In order to overcome some of these difficulties, we have built a simple multi-column system that is connected to an MS-MS instrument. Two independent chromatographs equipped with capillary columns were connected. The interface, which consists of a modified PTV injector, gives the possibilities of direct transfer, back-flushing, heart-cutting, intermediate cold trapping, trace enrichment and selective sample introduction. These operations are controlled by a switching valve system (DANI-MFC 393 unit). The chromatographic system was first connected to a MS-MS instrument which may result in high MS and collision activated MS spectra.     

Brief analysis of the retention process in RP-HPLC systems with a C(30) bonded stationary phase

The influence of the mobile-phase composition on the retention of eight model substances in different RP-HPLC systems with a C(30) alkyl bonded stationary phase has been studied. The aim of this study was to compare the performance of four valuable retention models assuming the partition and adsorption mechanism of retention. All the models were verified for different experimental data by four criteria: the sum of squared differences between the experimental and theoretical data; the approximation of the standard deviation; the Fisher test; and the F-test ratio.     

Chemical structures from the analysis of domain-averaged fermi holes. Nature of the Mn-Mn bond in bis(pentacarbonylmanganese)

Because of conflicting and contradictory classification based on traditional AIM characteristics, the nature of the Mn-Mn bond has been and still is the subject of continuing discussions. To overcome the existing inconsistencies in the interpretation of the nature of this bond, the bonding in Mn2(CO)10 has been analyzed and discussed in terms of new recently proposed methodology known as the analysis of domain-averaged Fermi holes. It has been shown that this analysis is able to reconcile the conflicting conclusions of earlier AIM-based studies with traditional anticipations based on simple electron counting rules. According to Fermi hole analysis, the Mn-Mn bond has the character of the more or less ordinary covalent single sigma bond, but the analysis also brings clear evidence in favor of Mn . . . (CO) intramolecular interactions between the metal atom and the ligands bonded to the other metal atom. These interactions could be responsible for the observed decrease of electron density at the bond critical point detected in AIM studies.     

Matrix effect in the analysis of drugs of abuse from urine with desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS) and desorption electrospray ionization-mass spectrometry (DESI-MS)

We have studied the matrix effect within direct analysis of benzodiazepines and opioids from urine with desorption electrospray ionization-mass spectrometry (DESI-MS) and desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS). The urine matrix was found to affect the ionization mechanism of the opioids in DAPPI-MS favoring proton transfer over charge exchange reaction. The sensitivity for the drugs in solvent matrix was at the same level with DESI-MS and DAPPI-MS (LODs 0.05–6 μg mL⁻¹) but the decrease in sensitivity due to the urine matrix was higher with DESI (typically 20–160-fold) than with DAPPI (typically 2–15-fold) indicating better matrix tolerance of DAPPI over DESI. Also in MS/MS mode, DAPPI provided better sensitivity than DESI for the drugs in urine. The feasibility of DAPPI-MS/MS was then studied in screening the same drugs from five authentic, forensic post mortem urine samples. A reference measurement with gas chromatography-mass spectrometry (GC–MS) (including pretreatment) revealed 16 findings from the samples, whereas with DAPPI-MS/MS after sample pretreatment, 15 findings were made. Sample pretreatment was found necessary, since only eight findings were made from the same samples untreated.     

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein

Full quantum computation of the electronic state of proteins has recently become possible by the advent of the ab initio fragment molecular orbital (FMO) method. We applied this method to the analysis of the interaction between the Bombyx mori pheromone-binding protein and its ligand, bombykol. The protein–ligand interaction of this molecular complex was minutely analyzed by the FMO method, and the analysis revealed several important interactions between the ligand and amino acid residues.     

Transients from a mixture of [(R(O)Sn)2C(CH3)2]2 and (RCl2Sn)2C(CH3)2 [R = (SiMe3)2CH]: an identification in situ by 1D 119Sn and 2D 1H?119Sn HMQC NMR spectroscopy and electrospray mass spectrometry

The reaction of the 2,2‐bis(organodichlorostannyl)propane [(Me₃Si)₂CH(Cl₂)Sn]₂CMe₂ (A) with the corresponding organotin oxide {[(Me₃Si)₂CH(O)Sn]₂CMe₂}₂ (B) does not provide the corresponding normally expected tetraorganodistannoxane {[(Me₃Si)₂CH(Cl)SnCMe₂Sn(Cl)CH(SiMe₃)₂]O}_n but a complex reaction mixture. One major product, namely the 2,4,6,8‐tetraorgano‐2,6‐dichloro‐1,5,9‐trioxa‐2,4,6,8‐tetrastannabicyclo[3.3.1]nonane derivative [(Me₃Si)₂CHSnCMe₂Sn(Cl)CH(SiMe₃)₂]₂O₃ (C) was identified in situ by 2D ¹H? ¹¹⁹Sn and ¹H? ¹³C heteronuclear multiple quantum coherence and heteronuclear multiple bond correlation NMR spectroscopy as well as electrospray mass spectrometry. Compound C is proposed to be in equilibrium with an ionic species C′, the cation of which has an adamantane‐type structure. Copyright © 2003 John Wiley & Sons, Ltd.     

Derivatization of (5R)-hydroxytriptolide from benzylamine to enhance mass spectrometric detection: application to a Phase I pharmacokinetic study in humans

(5R)-Hydroxytriptolide, a semisynthetic structural analog of triptolide, exhibits anti-inflammatory and immunosuppressive effect both in vitro and in vivo. The compound is currently undergoing Phase I clinical trials. This work describes the quantification of (5R)-hydroxytriptolide in human plasma based on chemical derivatization from benzylamine. Analysis through liquid chromatography–tandem mass spectrometry (LC–MS/MS) is performed for characterization. The primary reaction product between (5R)-hydroxytriptolide and benzylamine was identified as a 12,13-epoxide ring adduct. For quantification in plasma, (5R)-hydroxytriptolide and the internal standard (triptolide) were first extracted from diethyl ether–dichloromethane (3:2, v/v) and then converted to their benzylamine derivates at 80 °C for 1 h. The analytes are separated on a Gemini 5 μm 100 Å column, using a gradient elution program with a solvent consisting of 0.77 mM ammonium hydroxide (pH 10.0) and acetonitrile. An API 4000 tandem mass spectrometer operated in positive ion mode and equipped with an electrospray ionization source is used as detector. This method allows for a lower limit of quantification of 0.030 ng mL⁻¹. The validation results show accuracy (%RE < 11.7) and precision (%RSD < 8.6) at a broad linear dynamic range (0.030–100 ng mL⁻¹). The simple and quantitative derivatization coupled with tandem mass spectrometric analysis yields a sensitive and robust method for the quantification of (5R)-hydroxytriptolide in Phase I pharmacokinetic studies.     

Target Identification of 22-(4-Pyridinecarbonyl) Jorunnamycin A,a Tetrahydroisoquinoline Derivative from the Sponge Xestospongia sp., in Mediating Non-Small-Cell Lung Cancer Cell Apoptosis

A dysregulation of the cell-death mechanism contributes to poor prognosis in lung cancer. New potent chemotherapeutic agents targeting apoptosis-deregulating molecules have been discovered. In this study, 22-(4-pyridinecarbonyl) jorunnamycin A (22-(4′py)-JA), a synthetic derivative of bistetrahydroisoquinolinequinone from the Thai blue sponge, was semisynthesized by the Steglich esterification method, and its pharmacological mechanism in non-small-cell lung cancer (NSCLC) was elucidated by a network pharmacology approach. All predicted targets of 22-(4′py)-JA and genes related to NSCLC were retrieved from drug-target and gene databases. A total of 78 core targets were identified, and their associations were analyzed by STRING and Cytoscape. Gene ontology and KEGG pathway enrichment analyses revealed that molecules in mitogen-activated protein kinase (MAPK) signaling were potential targets of 22-(4′py)-JA in the induction of NSCLC apoptosis. In silico molecular docking analysis displayed a possible interaction of ERK1/2 and MEK1 with 22-(4′py)-JA. In vitro anticancer activity showed that 22-(4′py)-JA has strong cytotoxic and apoptosis-inducing effects in H460, H292 and A549 NSCLC cells. Furthermore, immunoblotting confirmed that 22-(4′py)-JA induced apoptotic cell death in an ERK/MEK/Bcl-2-dependent manner. The present study demonstrated that 22-(4′py)-JA exhibited a potent anticancer effect that could be further developed for clinical application and showed that network pharmacology approaches are a powerful tool to illustrate the molecular pathways of new drugs or compounds.     

Chemical properties of marine terpenoids. 1. Some reactions of (6S,10R)-10-bromo-3,11,11-trimethyl-7-methylidenespiro[5,5]undec-2-en-4-one,a sesquiterpenoid from the sea hare Aplysia dactylomela

The structures of products obtained by reductive debromination and CF₃COOH- and KOH-induced transformations of natural chamigrane-type sesquiterpenoid (6S,10R)-10-bromo-3,11,11-trimethyl-7-methylidenespiro[5,5]undec-2-en-4-one (dactylone) isolated from the sea hare Aplysia dactylomela were analyzed. The absolute configurations of the reaction products were established by CD spectra taking into account the configuration of the starting dactylone.