Fast characterization of intact proteins using a high-throughput eight-channel parallel liquid chromatography/mass spectrometry system

The preparation of protein substrates requires that a large number of chromatographic fractions be analyzed for the presence of reactants, products and by-products. Analyses using linear matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) or single column liquid chromatography/mass spectrometry (LC/MS) have been inadequate because of mass resolution or throughput. Therefore, a high-throughput method employing an eight-channel parallel reverse-phase LC/MS system was developed. This system is capable of screening fractions from preparative ion-exchange chromatography with the required mass accuracy and throughput so that the protein purification process can be monitored in a relatively short period of time. As an example, the purification and analysis of an acylated protein with a molecular weight of 8.9 kDa is described and the detection of a contaminating by-product that differs in size by less than 20 Da is demonstrated. Using the current instrumentation and approach, it is practical to analyze 50 protein-containing fractions from column chromatography in less than 1 hour using parallel LC/MS.     

Screening of antioxidant phenolic compounds in Chinese Rhubarb combining fast counter‐current chromatography fractionation and liquid chromatography/mass spectrometry analysis

In this paper, an effective method combing fast elution‐extrusion counter‐current chromatography (CCC) and LC/MS for rapid screening of antioxidative phenolic compounds in Chinese Rhubarb is presented. An integrated three‐coil CCC column (40 mL each coil) was used to accomplish the optimization of biphasic liquid system. In a single run (approximately 40 min), the solvent system composed of n‐hexane/ethyl acetate/methanol/water (1:1:1:1, v/v) was selected as optimum CCC liquid system for fast fractionation of the crude ethanol extract. With a 140 mL‐capacity CCC instrument, 100 mg Chinese Rhubarb extract was separated under the optimized conditions, producing six fractions in only 100 min. The quantities of each fraction were ～15 mg. In addition, each fraction was subjected to antioxidant activity assay and characterized by LC/MS analysis. Fifty compounds, including phenolic acids, phenolic glucosides and hydroxyanthraquinones, were detected by LC/MS/MS analysis. As a result, gallic acid together with Fr I showed excellent antioxidant activity, which was well consistent with previous studies and exhibited great potential for natural drug discovery program of the present method.     

LC/ESI‐MS/MS characterisation of lipopeptide biosurfactants produced by the Bacillus licheniformis V9T14 strain

Lipopeptide biosurfactants produced by the Bacillus licheniformis V9T14 strain showed an interesting anti‐adhesion activity against biofilm formation of human pathogenic bacterial strains. The chemical characterisation of the crude extract of V9T14 strain was first developed through electrospray ionisation mass spectrometry (ESI‐MS) and ESI‐MS/MS direct infusions: two sets of molecular ion species belonging to the fengycin and surfactin families were revealed and their structures defined, interpreting their product ion spectra. The LC/ESI‐MS analysis of the crude extract allowed to separate in different chromatogram ranges the homologues and the isoforms of the two lipopeptide families. The extract was then fractionated by silica gel chromatography in two main fractions, I and II. The purified biosurfactants were analysed through a new, rapid and suitable LC/ESI‐MS/MS method, which allowed characterising the composition and the structures of the produced lipopeptides. LC/ESI‐MS/MS analysis of fraction I showed the presence of C₁₃, C₁₄ and C₁₅ surfactin homologues, whose structures were confirmed by the product ion spectra of the sodiated molecules [M + Na]⁺ at m/z 1030, 1044 and 1058. LC/ESI‐MS/MS analysis of fraction II confirmed the presence of two main fengycin isoforms, with the protonated molecules [M + H]⁺ at m/z 1478 and 1506 corresponding to C₁₇ fengycin A and C₁₇ fengycin B, respectively. Other homologues (C₁₄ to C₁₆) were revealed and confirmed as belonging to fengycin A or B according to the retention times and the product ions generated, although with the same nominal mass. Finally, a relative percentage content of each homologue for both lipopeptides families in the whole extract was proposed. Copyright © 2010 John Wiley & Sons, Ltd.     

Two-dimensional liquid chromatography-capillary zone electrophoresis-sheathless electrospray ionization-mass spectrometry: evaluation for peptide analysis and protein identification

A peptide separation strategy that combines two-dimensional (2-D) liquid chromatography (LC)-capillary zone electrophoresis (CZE) with tandem mass spectrometry (MS/MS) is described for the identification of proteins in complex mixtures. To test the effectiveness of this strategy, a serum sample was depleted of the high-abundance proteins by methanol precipitation, digested with trypsin to generate a complex peptide mixture, and separated into 96 fractions by reversed-phase (RP)-LC. Compared to ion-exchange LC separations, RPLC provides much higher resolution and peak capacity. Fractions were collected off-line from the RPLC separation, and subjected to short 20 min CZE separations. The separated zones were introduced to the mass spectrometer through a sheathless electrospray ionization interface that is integrated on the separation capillary. The ease of fabrication of the interface and its durability allowed for the analysis of all fractions on a single capillary in a relatively short analysis time. A stable electrospray was produced at nanoliter flowrates by augmenting analyte electrophoretic and electroosmotic mobilities with pressure-assisted flow. Unlike first-dimensional ion-exchange LC fractionation, where there is a large degree of overlap, the CZE-MS results show less than 15% overlap between neighboring RPLC fractions.     

Analysis of proteins from a glioma cell line by using micro-scale solution isoelectric focusing in combination with liquid chromatography/tandem mass spectrometry

In this study we have investigated whether micro-solution isoelectric focusing (microsol-IEF) can be used as a pre-fractionation step prior to liquid chromatography/tandem mass spectrometry (LC/MS/MS) and if extensive sample purification of the different fractions is required. We found that, in spite of the high concentrations of buffer and detergents, no clean up of the digested microsol-IEF fractions was necessary before analysis by LC/MS/MS. We also concluded that it is possible to identify at least twice as many proteins in a glioma cell lysate with the combination of microsol-IEF and LC/MS/MS than with LC/MS/MS alone. Furthermore, most of the proteins that were identified from one microsol-IEF fraction by using analytical narrow-range two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and peptide mass fingerprinting with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) were also identified by LC/MS/MS. Finally, we used the combination of microsol-IEF and LC/MS/MS to compare two sample preparation methods for glioma cells and found that several nuclear, mitochondria, and endoplasmic reticulum proteins were only present in the sample that had been subjected to lipid extraction by incubating the homogenized cells in chloroform/methanol/water.     

Preparation of a stationary phase with quaternary ammonium embedded group for selective separation of alkaloids based on ion‐exclusion interaction

A stationary phase (named QA C10) with quaternary ammonium embedded between a propyl and a decyl chain was synthesized by immobilization of N,N‐dimethyldecylamine on chloropropyl–silica surface. A set of representative neutral, basic, and acidic compounds was employed to evaluate its chromatographic properties. The results illustrated that QA C10 was a mixed‐mode stationary phase possessing both hydrophobic and ionic characteristics. The QA C10 stationary phase was further used for selective separation of alkaloids from Cortex phellodendri. Under acidic condition, alkaloids could be eluted in first 8 min, while other neutral and acidic fractions were retained better on QA C10 column. Then, obtained alkaloid fraction was analyzed by LC‐MS/MS and 22 alkaloids were identified. Our study confirmed the advantages and application potential of the QA C10 stationary phase for alkaloids separation.     

Determination of14C in spent moderator ion-exchange resin from Bruce Nuclear Generating Station A

Spent ion-exchange resins are produced in the purification of coolant and moderator systems during the normal operation of CANDU (Canada deuterium uranium) nuclear reactors. Carbon-14 is a radionuclide of concern in disposal of ion-exchange resins because of its relatively long half-life, its potential high mobility and its ability to be easily incorporated into organisms. Only limited data are presently available on the¹⁴C concentrations of spent from CANDU reactors. To establish a more comprehensive datahase for this radionuclide, concentrations of¹⁴C were determined for two moderator resins from Bruce Nuclear Generating Station A. Mixed bed resins were separated into anion and cation fractions using a sugar solution, and the¹⁴C concentrations were determined for each fraction. Carbon-14-was located predominantly on the anion beads. Samples of anion resin were found to undergo an 81% loss in the¹⁴C concentration over a period of 160 d following the sugar separation procedure. Some evidence is given to suggest this loss in¹⁴C may result from microbial activity. Concentrations and distributions of other predominant radionuclides, such as⁶⁰Co and¹⁵³Gd, are discussed as well.     

Off‐line 2‐D RPLC/RPLC method for separation of components in Dalbergia odorifera T. Chen

An off‐line 2‐D RPLC/RPLC system incorporating a β‐CD based column and a BEH C18 column was developed in the separation of components in Dalbergia odorifera T. Chen. (Jiang Xiang). Both orthogonality and van Deemter curves of the two columns were investigated. The orthogonality was about 57%, which was evaluated with 40 standard solutes. Optimized column efficiency could be achieved under optimal linear velocity (0.04 cm/s) on the CD column or under high linear velocity (0.32 cm/s) on the BEH C18 column. With the 2‐D LC system, totally 637 peaks were separated in 114 fractions from the extraction of Jiang Xiang. Meanwhile, 19 flavanoids were tentatively identified from 114 fractions with Q‐TOF MS. The results demonstrated the separation power of this 2‐D LC system and further proved the high orthogonality between CD and C18 columns.     

Multidimensional liquid chromatography with parallel ICP MS and electrospray MS/MS detection as a tool for the characterization of arsenic species in algae

An analytical strategy was developed for the characterization of arsenic species in a Laminaria algae. The approach was based on multidimensional liquid chromatography (LC) including sample extract cleanup by size-exclusion LC, separation of arsenic species by anion-exchange LC, verification of the chromatographic purity of arsenic-containing fractions, and their further purification, if necessary, by reversed-phase (RP) HPLC. The complementarity of ICP MS, used as the chromatographic detector, and ES MS/MS, employed for the identification of the peaks observed, was demonstrated. The species found were: arsenosugar A 11.7+/-0.5 microg g(-1), AsV 10.9+/-2.1 microg g(-1), arsenosugar B 2.22+/-0.07 microg g(-1), arsenosugar D 1.5+/-1.2 microg g(-1), a newly detected arsenosugar 1.13+/-0.07 microg g(-1), arsenosugar C 0.61+/-0.04 microg g(-1), DMA 0.42+/-0.02 microg g(-1) and these accounted for >99% of the arsenic present. The identities of all the species, except the newly detected compound, were doubly checked by matching the retention times of chromatographically pure (after the 3rd LC dimension) species with standards and by ES MS/MS.     

Application of micro-electrospray liquid chromatography techniques to FT-ICR MS to enable high-sensitivity biological analysis

A microbore electrospray (ESI) injection system has been adapted to our 9.4-tesla ESI FT-ICR mass spectrometer, greatly enhancing the stability and sensitivity of the system. Spray was generated from micro-ESI needles made from sharply tapered, polished fused silica capillaries of 25 to 50 µm inner diameter. Micro-ESI permits low-level sample analysis by constant infusion at sub-µL/min flow rate over a wide range of solvent conditions in both positive- and negative-ion mode. The system is flexible and allows rapid conversion to allow routine LC/MS analysis on low-level mixtures presented in biological media. LC/MS analyses were accomplished by replacing micro-ESI needles with capillaries packed with reverse phase retention media to permit analyte concentration and purification prior to analysis (micro-ESI/LC). A unique nano-flow LC pumping system was developed, capable of producing a true unsplit solvent gradient at flow rates below 1 µL/min. The micro-ESI/LC FT-ICR system produces mass spectra from a mixture of three neuroactive peptides at a concentration of 500 amol/µL (5 fmol each total loaded) in biological salts with baseline separation, signal-to-noise ratio of >10:1 and mass resolving power >5000. These results represent a reduction in detection limit by a factor of ～2 × 10⁶ over the best previously published LC/FT-ICR MS data.     

Combined usage of cascade affinity fractionation and LC‐MS/MS for the proteomics of adult mouse testis

In this report, the proteomics of adult mouse testis were analyzed by the combined usage of cascade affinity fractionation and LC‐MS/MS. The differences between the selected affinity ligands in size, shape, structure, and biochemical characteristics, result in each ligand exhibiting a specific affinity to some protein groups. Therefore, a cascade composition of different ligands can be applied to the fractionation of complex tissue proteins. Ultimately, the fractions collected from cascade affinity fractionation were analyzed by LC‐MS/MS, which resulted in high confidence identification of a total of 1378 non‐redundant mouse testis protein groups, over 2.6 times as many proteins as were detected in the un‐fractionated sample (526). All detected proteins were bioinformatically categorized according to their physicochemical characteristics (such as relative molecular mass, pI, grand average hydrophobicity value, and transmembrane helices), subcellular location, and function annotation. This approach highlighted the sensitivity of this method to a wide variety of protein classes. Utilizing a combination of cascade affinity fractionation and LC‐MS/MS, we have established the largest proteomic database for adult mouse testis at the present time.     

Comprehensive identification and structural characterization of target components from Gelsemium elegans by high‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry based on accurate mass databases combined with MS/MS spectra

This study reports an applicable analytical strategy of comprehensive identification and structure characterization of target components from Gelsemium elegans by using high‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry (LC‐QqTOF MS) based on the use of accurate mass databases combined with MS/MS spectra. The databases created included accurate masses and elemental compositions of 204 components from Gelsemium and their structural data. The accurate MS and MS/MS spectra were acquired through data‐dependent auto MS/MS mode followed by an extraction of the potential compounds from the LC‐QqTOF MS raw data of the sample. The same was matched using the databases to search for targeted components in the sample. The structures for detected components were tentatively characterized by manually interpreting the accurate MS/MS spectra for the first time. A total of 57 components have been successfully detected and structurally characterized from the crude extracts of G. elegans , but has failed to differentiate some isomers. This analytical strategy is generic and efficient, avoids isolation and purification procedures, enables a comprehensive structure characterization of target components of Gelsemium and would be widely applicable for complicated mixtures that are derived from Gelsemium preparations. Copyright © 2017 John Wiley & Sons, Ltd.     

Biosynthesis of Bromoroquefortines in a High Saline Medium by Penicillium chrysogenum,a Terrestrial Endophyte Collected from Coffea arabica

Roquefortine C ( 1 ) and 11‐bromoroquefortine C ( 4 ) were isolated from Penicillium chrysogenum, an endophyte obtained from green leaves of Coffea arabica, during induction experiments by adding halide salts to the culture media. In our studies, 11‐bromoroquefortine D and 11‐bromo‐17‐hydroxybromoroquefortine C were identified by LC/HR‐MS. It is the first time that bromoroquefortine C and D are described as halogenated natural products. These halo alkaloids were shown to be biosynthesized from brominated tryptophan as the biosynthetic precursor. Cytotoxic and antibiotic assays using roquefortine C and 11‐bromoroquefortine C showed that the presence of the 11‐Br substituent impairs some biological activities of this alkaloid.     

Structural investigation and elucidation of new communesins from a marine‐derived Penicillium expansum Link by liquid chromatography/electrospray ionization mass spectrometry

Penicillium expansum is a ubiquitous species for which there are only few reports for chemical investigation in marine environments. Among the numerous secondary metabolites produced by this species, communesins represent a new class of cytotoxic and insecticidal indole alkaloids. In this study, we investigated a marine P. expansum strain exhibiting neuroactivity on a Diptera larvae bioassay. Bio‐guided purification led to the isolation and the identification of communesin B as the main active compound by HRMS and ¹H and ¹³C NMR. Liquid chromatography analyses with detection by electrospray ionization coupled with tandem mass spectrometry (LC/ESI‐MS/MS) and high‐resolution tandem mass spectrometry (LC/HRMS/MS) allowed the identification and characterization of four other known communesins (A, D, E and F) in the crude extract. A fragmentation model for dimethyl epoxide communesins was proposed after detailed interpretation of their MS/MS spectra. Further analyses of the extract using the modelled fragmentations led to the detection of seven new communesins found as minor compounds. Chemical structural elucidation of these new derivatives is discussed based on their fragmentation characteristics. Copyright © 2009 John Wiley & Sons, Ltd.     

A Nano-Chip-LC/MS<Superscript><Emphasis Type="Italic">n</Emphasis></Superscript> Based Strategy for Characterization of Modified Nucleosides Using Reduced Porous Graphitic Carbon as a Stationary Phase

LC/MS analysis of ribonucleosides is traditionally performed by reverse phase chromatography on silica based C18 type stationary phases using MS compatible buffers and methanol or acetonitrile gradients. Due to the hydrophilic and polar nature of nucleosides, down-scaling C18 analytical methods to a two-column nano-flow setup is inherently difficult. We present a nano-chip LC/MS ion-trap strategy for routine characterization of RNA nucleosides in the fmol range. Nucleosides were analyzed in positive ion mode by reverse phase chromatography using a 75 μ × 150 mm, 5 μ particle porous graphitic carbon (PGC) chip with an integrated 9 mm, 160 nL trapping column. Nucleosides were separated using a formic acid/acetonitrile gradient. The method was able to separate isobaric nucleosides as well as nucleosides with isotopic overlap to allow unambiguous MS ⁿ identification on a low resolution ion-trap. Synthesis of 5-hydroxycytidine (oh⁵C) was achieved from 5-hydroxyuracil in a novel three-step enzymatic process. When operated in its native state using formic acid/acetonitrile, PGC oxidized oh⁵C to its corresponding glycols and formic acid conjugates. Reduction of the PGC stationary phase was achieved by flushing the chip with 2.5 mM oxalic acid and adding 1 mM oxalic acid to the online solvents. Analyzed under reduced chromatographic conditions oh⁵C was readily identified by its MH⁺ m/z 260 and MSⁿ fragmentation pattern. This investigation is, to our knowledge, the first instance where oxalic acid has been used as an online reducing agent for LC/MS. The method was subsequently used for complete characterization of nucleosides found in tRNAs using both PGC and C18 chips.     

Synthesis,Characterization, and Molecular Docking Study of Some Novel Imidazole Derivatives as Potential Antifungal Agents

The azole pharmacophore is still regarded as a viable lead structure for the synthesis of more effective antifungal agents. In this study, two novel series of imidazole derivatives containing dithiocarbamate (5a–5g) and (benz)azolethiol (6a–6n) side chains that are structurally related to the famous antifungal azole pharmacophore were synthesized, and the structures of them were characterized by spectral (IR, ¹H NMR, ¹³C NMR, and MS spectra) analyses. The synthesized compounds were screened in vitro antifungal activity against pathogenic strains fungi. Theoretical ADME (absorption, distribution, metabolism, and excretion) predictions were calculated for final compounds. A molecular docking study of the most active compound with target “lanosterol 14α‐demethylase” (CYP51) was performed to unravel the mode of antifungal action. Compound 5e , which features imidazole and 4‐methoxybenzyl piperazine scaffolds, showed the most promising antifungal activity with an MIC₅₀ value of 0.78 μg/mL against C. krusei. Effect of the compound 5e against ergosterol biosynthesis was observed by LC–MS–MS method, which is based on quantification of ergosterol level in C. krusei.     

Determination of human muscle protein fractional synthesis rate: an evaluation of different mass spectrometry techniques and considerations for tracer choice

In the present study, different MS methods for the determination of human muscle protein fractional synthesis rate (FSR) using [ring‐¹³C₆]phenylalanine as a tracer were evaluated. Because the turnover rate of human skeletal muscle is slow, only minute quantities of the stable isotopically labeled amino acid will be incorporated within the few hours of a typical laboratory experiment. GC combustion isotope ratio MS (GC‐C‐IRMS) has thus far been considered the ‘gold’ standard for the precise measurements of these low enrichment levels. However, advances in liquid chromatography‐tandem MS (LC‐MS/MS) and GC‐tandem MS (GC‐MS/MS) have made these techniques an option for human muscle FSR measurements. Human muscle biopsies were freeze dried, cleaned, and hydrolyzed, and the amino acids derivatized using either N‐acetyl‐n‐propyl, phenylisothiocyanate, or N‐methyl‐N‐(tert‐butyldimethylsilyl)trifluoroacetamide (MTBSTFA) for GC‐C‐IRMS, LC‐MS/MS, and GC‐MS/MS analysis, respectively. A second derivative, heptafluorobutyric acid (HFBA), was also used for GC‐MS/MS analysis as an alternative for MTBSTFA. The machine reproducibility or the coefficients of variation for delta tracer‐tracee‐ratio measurements (delta tracer‐tracee‐ratio values around 0.0002) were 2.6%, 4.1%, and 10.9% for GC‐C‐IRMS, LC‐MS/MS, and GC‐MS/MS (MTBSTFA), respectively. FSR determined with LC‐MS/MS compared well with GC‐C‐IRMS and so did the GC‐MS/MS when using the HFBA derivative (linear fit Y = 1.08 ± 0.10, X + 0.0049 ± 0.0061, r = 0.89 ± 0.01, P < 0.0001). In conclusion, (1) IRMS still offers the most precise measurement of human muscle FSR, (2) LC‐MS/MS comes quite close and is a good alternative when tissue quantities are too small for GC‐C‐IRMS, and (3) If GC‐MS/MS is to be used, then the HFBA derivative should be used instead of MTBSTFA, which gave unacceptably high variability. Copyright © 2014 John Wiley & Sons, Ltd.     

Liquid chromatography/mass spectrometry‐based plasma metabolic profiling study of escitalopram in subjects with major depressive disorder

Liquid chromatography‐mass spectrometry (LC‐MS) method revealed the plasma metabolite profiles in major depressive disorder patients treated with escitalopram (ECTP) (n = 7). Depression severity was assessed according to the 17‐item Hamilton Depression Rating Scale. Metabolic profiles were derived from major depressive disorder subject blood samples collected after ECTP treatment. Blood plasma was separated and processed in order to effectively extract metabolites, which were then analyzed using LC‐MS. We identified 19 metabolites and elucidated their structures using LC‐tandem MS (LC‐MS/MS) combined with elemental compositions derived from accurate mass measurements. We further used online H/D exchange experiments to verify the structural elucidations of each metabolite. Identifying molecular metabolites may provide critical insights into the pharmacological and clinical effects of ECTP treatment and may also provide useful information informing the development of new antidepressant treatments. These detailed plasma metabolite analyses may also be used to identify optimal dose concentrations in psychopharmacotherapeutic treatment through drug monitoring, as well as forming the basis for response predictions in depressed subjects.     

Analysis of β‐blockers in groundwater using large‐volume injection coupled‐column reversed‐phase liquid chromatography with fluorescence detection and liquid chromatography time‐of‐flight mass spectrometry

Atenolol, nadolol, metoprolol, bisoprolol and betaxolol were simultaneously determined in groundwater samples by large‐volume injection coupled‐column reversed‐phase liquid chromatography with fluorescence detection (LVI‐LC‐LC‐FD) and liquid chromatography‐time‐of‐flight mass spectrometry (LC‐TOF‐MS). The LVI‐LC‐LC‐FD method combines analyte isolation, preconcentration and determination into a single step. Significant reductions in costs for sample pre‐treatment (solvent and solid phases for clean up) and method development times are also achieved. Using LC‐TOF‐MS, accurate mass measurements within 3 ppm error were obtained for all of the β‐blockers studied. Empirical formula information can be obtained by this method, allowing the unequivocal identification of the target compounds in the samples. To increase the sensitivity, a solid‐phase extraction step with Oasis MCX cartridge was carried out yielding recoveries of 79–114% (n=5) with RSD 2–7% for the LC‐TOF‐MS method. SPE gives a high purification of β‐blockers compared with the existing methods. A 100% methanol wash was allowed for these compounds with no loss of analytes. Limit of quantification was 1–7 ng/L for LVI‐LC‐LC‐FD and 0.25–5 ng/L for LC‐TOF‐MS. As a result of selective extraction and effective removal of coextractives, no matrix effect was observed in LVI‐LC‐LC‐FD and LC‐TOF‐MS analyses. The methods were applied to detect and quantify β‐blockers in groundwater samples of Almería (Spain).