Detection of functional ricin by immunoaffinity and liquid chromatography-tandem mass spectrometry

The toxin ricin is a biological weapon that may be used for bioterrorist purposes. As a member of the group of ribosome-inactivating proteins (RIPs), ricin has an A-chain possessing N-glycosidase activity which irreversibly inhibits protein synthesis. In this paper, we demonstrate that provided appropriate sample preparation is used, this enzymatic activity can be exploited for functional ricin detection with sensitivity similar to the best ELISA and specificity allowing application to environmental samples. Ricin is first captured by a monoclonal antibody directed against the B chain and immobilized on magnetic beads. Detection is then realized by determination of the adenine released by the A chain from an RNA template using liquid chromatography coupled to tandem mass spectrometry. The immunoaffinity step combined with the enzymatic activity detection leads to a specific assay for the entire functional ricin with a lower limit of detection of 0.1 ng/mL (1.56 pM) after concentration of the toxin from a 500 microL sample size. The variability of the assay was 10%. Finally, the method was applied successfully to milk and tap or bottled water samples.     

A method for quantitatively differentiating crude natural extracts using high-performance liquid chromatography-electrospray mass spectrometry

This paper describes a method for quantitatively differentiating crude natural extracts using high-performance liquid chromatography-electrospray mass spectrometry (HPLC-ESI-MS). The method involves performing an HPLC-MS analysis using standard reversed-phase C18 gradient separation on the crude extract. The HPLC system used in this study was a dual-column system designed to optimize throughput. Using image analysis techniques, the data are reduced to a list containing the m/z value and retention time of each ion. The ion lists are then compared in a pairwise fashion to compute a sample similarity index between two samples. The similarity index is based on the number of ions common to both and is scaled from 0 to 1. Extract controls were analyzed throughout a run of 88 unknown fungal extracts. The controls provided information about column and spectrometer stability and overall sensitivity. Pairwise comparison of all control samples indicates that the similarity index is high (0.8) for replicate samples. Comparison between the unknown extract samples produces a distribution of similarities ranging from replicates (0.8) to very dissimilar (0.1). This information can be used to judge the chemical diversity of natural extract samples, which is one approach to determining the quality of libraries being used for drug discovery via high-throughput screening.     

Detection and quantification of ricin in beverages using isotope dilution tandem mass spectrometry

The toxic plant protein ricin has gained notoriety due to wide availability and potential use as a bioterrorism agent, with particular concern for food supply contamination. We have developed a sensitive and selective mass spectrometry-based method to detect ricin in tap water, 2% milk, apple juice, and orange juice. Ricin added to beverage matrices was extracted using antibody-bound magnetic beads and digested with trypsin. Absolute quantification was performed using isotope dilution mass spectrometry with a linear ion trap operating in product-ion-monitoring mode. The method allows for identification of ricin A chain and B chain and for distinction of ricin from ricin agglutinin within a single analytical run. Ricin-bound beads were also tested for deadenylase activity by incubation with a synthetic ssDNA oligomer. Depurination of the substrate by ricin was confirmed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOFMS). This method was used successfully to extract ricin from each beverage matrix. The activity of recovered ricin was assessed, and quantification was achieved, with a limit of detection of 10 fmol/mL (0.64 ng/mL).     

Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures

We report a new tandem mass spectrometric approach for the improved identification of polypeptides from mixtures (e.g., using genomic databases). The approach involves the dissociation of several species simultaneously in a single experiment and provides both increased speed and sensitivity. The data analysis makes use of the known fragmentation pathways for polypeptides and highly accurate mass measurements for both the set of parent polypeptides and their fragments. The accurate mass information makes it possible to attribute most fragments to a specific parent species. We provide an initial demonstration of this multiplexed tandem MS approach using an FTICR mass spectrometer with a mixture of seven polypeptides dissociated using infrared irradiation from a CO2 laser. The peptides were added to, and then successfully identified from, the largest genomic database yet available (C. elegans), which is equivalent in complexity to that for a specific differentiated mammalian cell type. Additionally, since only a few enzymatic fragments are necessary to unambiguously identify a protein from an appropriate database, it is anticipated that the multiplexed MS/MS method will allow the more rapid identification of complex protein mixtures with on-line separation of their enzymatically produced polypeptides.     

High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry

Direct injection of samples on high-resolving mass spectrometers is an effective way to maximize analytical throughput and yet allow analyte discrimination in complex samples by mass-to-charge ratio. We present a platform of flow injection electrospray-time-of-flight mass spectrometry to profile small molecules in >1400 biological extracts per day at native mass resolution. We comprehensively benchmark the performance with more than 5000 injections of chemically defined standards and Escherichia coli cellular extracts obtained from miniscale cultivations. For at least 90% of tested compounds, we attain a linear response over 3 decades of concentration, interday coefficient of variation of <20%, and a mass accuracy of <0.001 amu. In polar Escherichia coli fractions, we reproducibly detected >1500 distinct ions in each mode. The accurate mass and correlation analysis enabled one to assign with good confidence 400-800 ions to electrospray derivatives of metabolites listed in the genome-wide reconstruction of Escherichia coli metabolism. Hence, we attain a coverage of about one-quarter of the total number of compounds listed in the reconstruction. Finally, we present an exemplary screen with Escherichia coli deletion mutants to show the exquisite capacity of the platform to identify lesions in primary metabolism at high throughputs.     

Microorganism identification by mass spectrometry and protein database searches.

A method for rapid identification of microorganisms is presented, which exploits the wealth of information contained in prokaryotic genome and protein sequence databases. The method is based on determining the masses of a set of ions by MALDI TOF mass spectrometry of intact or treated cells. Subsequent correlation of each ion in the set to a protein, along with the organismic source of the protein, is performed by searching an Internet-accessible protein database. Convoluting the lists for all ions and ranking the organisms corresponding to matched ions results in the identification of the microorganism. The method has been successfully demonstrated on B. subtilis and E. coli, two organisms with completely sequenced genomes. The method has been also tested for identification from mass spectra of mixtures of microorganisms, from spectra of an organism at different growth stages, and from spectra originating at other laboratories. Experimental factors such as MALDI matrix preparation, spectral reproducibility, contaminants, mass range, and measurement accuracy on the database search procedure are addressed too. The proposed method has several advantages over other MS methods for microorganism identification.     

Direct analysis of silica gel extracts from immunostained glycosphingolipids by nanoelectrospray ionization quadrupole time-of-flight mass spectrometry

A combined strategy of preparative high-performance thin-layer chromatography overlay assay and mass spectrometry was established for the structural characterization of immunostained glycosphingolipids (GSLs) in silica gel extracts. Crude chloroform/methanol/water (30/60/8, v/v/v) extracts of immunostained TLC bands were analyzed by nanoelectrospray low-energy CID mass spectrometry without further purification. The GSL species investigated were isomeric monosialogangliosides of the neolacto series from a ganglioside preparation of human granulocytes, the disialoganglioside GD3 from a human melanoma lipid extract, and ganglio series Gg3Cer of a neutral GSL preparation from murine lymphoreticular MDAY-D2 cells. For the specific detection of lipid-bound oligosaccharides, polyclonal chicken IgY, murine monoclonal IgG3, and IgM antibodies were used. The resulting mass spectra show that only analytical quantities of approximately 1 microg of a single GSL within a complex mixture are required for the structure determination of immunostained GSLs by MS and MS/MS. All species investigated were detected as singly charged deprotonated molecular ions, and neither buffer-derived salt adducts nor coextracted contaminants from the immunostaining procedure or the silica gel layer were observed. This effective HPTLC-MS-joined procedure offers a wide range of applications for any carbohydrate binding agents such as bacterial toxins, plant lectins, and others.     

Quantification of diacylglycerol species from cellular extracts by electrospray ionization mass spectrometry using a linear regression algorithm

Diacylglycerols (DAGs) play significant roles in both intermediate metabolism and signal transduction. These lipid species are second messengers involved in modulating a plethora of cellular processes. Evaluation of DAG species concentrations has been hampered by the lack of a reliable method for molecular species analysis within a complex mixture of cellular lipids. We describe a new method for quantitative analysis of DAG species from complex biological extracts based on positive mode electrospray ionization mass spectrometry without prior derivatization. Quantification is achieved using internal standards and calibration curves constructed by spiking cell extracts with different concentrations of DAG species containing various acyl chain lengths and degrees of unsaturation. The new mass spectral data processing algorithm incorporates a multiple linear regression model including a factor accountable for possible interactions between experimental preparations and the slope of the curve for the standards, allowing the examinations of the effects of sample origin conditions (such as cell types, phenotypes, etc.) and instrument variability on this slope. Internal standards provide a basis for quantification of 28 DAG molecular species detected in RAW 264.7 cells after stimulation of a G-protein coupled receptor with platelet activating factor. This method displays excellent reproducibility over the established range of concentrations with variations of < or =10% and is highly sensitive with a detection limit of 0.1-0.4 pmol/microL depending upon acyl chain composition. We have shown differential effects on various DAGs in response to a ligand which illustrates the importance of examining lipids at the molecular species level rather than as a single homogeneous entity.     

Characterization of toxins within crude venoms by combined use of Fourier transform mass spectrometry and cloning

The standard analytical procedure for screening the proteomic profile of a venom often relies on an appropriate combination of sample extraction, electrophoresis, reversed-phase high-performance liquid chromatography, mass spectrometry, and Edman degradation. We present in this study a new approach for venom screening based on Fourier transform mass spectrometry (FTMS) analysis directly on the crude venom. The venom chosen is a unique sample from Atractaspis irregularis, a species never studied at the molecular level previously. This snake belongs to the Atractaspidae family that is known to produce highly toxic venoms containing endothelin-like peptides called sarafotoxins (SRTXs). Nanoelectrospray-FTMS spectrum of the crude venom allowed the identification of 60 distinct compounds with molecular masses from 600 to 14,000 Da, which would have been impossible without the resolution of this kind of instrument. De novo sequencing within the entire venom confirmed the sequences of two new families of sarafotoxins, whose precursors had been cloned, and allowed the characterization of a third one. One particularly interesting point was that the propolypeptides appeared processed not in one unique compound, but rather in different length molecules ranging from 15 for the shorter to 30 amino acids for the longer. Moreover, our results clearly establish that in the case of A. irregularis only one copy of mature sarafotoxin emerges from each precursor, which is a totally different organization in comparison of other precursors of SRTXs.     

Testing the significance of microorganism identification by mass spectrometry and proteome database search

We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for deltam = +/-1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the cluttered and incomplete nature of the data, it is likely that neither simple ranking nor simple hypothesis testing will be sufficient for truly robust microorganism identification over a large number of candidate microorganisms.     

Direct analysis and identification of Helicobacter and Campylobacter species by MALDI-TOF mass spectrometry.

Campylobacter jejuni, Campylobacter fetus, and Campylobacter coli were compared with Helicobacter pylori and Helicobacter mustelae by direct analysis of individual cultured colonies in 50% methanol-water with a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS). H. pylori and Campylobacter species from blood agar culture produced unique, complex spectra with over 25 different ions in mass/charge (m/z) range from 2,000 to 62,000. A biomarker for H. pylori was centered around m/z 58,268, and H. mustelae was distinguished from H. pylori by its ions at m/z 49,608 and 57,231. Campylobacters could be distinguished from Helicobacters by their lack of ions around m/z 58,000 and 61,000 as well as distinguishing biomarkers of lower m/z: 10,074 and 25,478 for C. coli; m/z 10,285 and 12,901 for C. jejuni; m/z 10,726 and 11,289 for C. fetus. MALDI-TOF MS is a rapid and direct method for detection of these potentially pathogenic bacteria from culture.     

Speciation and identification of organoselenium metabolites in human urine using inductively coupled plasma mass spectrometry and tandem mass spectrometry

A method for speciation and identification of organoselenium metabolites found in human urine samples using high performance liquid chromatography/inductively coupled plasma mass spectrometry (HPLC/ICP-MS) and tandem mass spectrometry (MS/MS) is described. Reversed-phase chromatographic separation was used for sample fractionation with the ICP-MS functioning as an element-selective detector, and six distinct selenium-containing species were detected in a human urine sample. Fractions were then collected and analyzed using a triple quadrupole mass spectrometer with electrospray ionization and collision-induced dissociation to obtain structural information. The first two fractions were identified specifically as selenomethionine and selenocystamine, estimated to be present at approximately 11 and 40 ppb, respectively. To the best of our knowledge, this is the first time these two metabolites have been positively identified in human urine.     

Gender identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A rapid, simple, and reliable gender determination of human DNA samples was successfully obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Detection sensitivity reached 0.01 ng or less for DNA samples.     

Liquid chromatography online with selected reaction monitoring electrospray mass spectrometry for the determination of organoarsenic species in crude extracts of marine reference materials

The large number of arsenic species known to be present in marine samples and their broad range of chemical properties pose a significant challenge for arsenic speciation analysis. The predominantly used ICPMS detection online with HPLC only provides element-selective information, which is not sufficient for the identification of arsenic species without standards. However, electrospray tandem mass spectrometry in the selected reaction monitoring (SRM) mode enables molecule-selective detection with high sensitivity for quantification. A new HPLC-ES-SRM method was developed for the determination of more than 20 organoarsenic species. Two chromatographic systems were compared, an anion exchange method and a combined cation anion exchange method. Collision-induced dissociation breakdown curves were constructed for all arsenic species investigated and used to optimize the SRM conditions. External calibration was performed with mixed standard solutions containing 21 arsenic species. Two SRM transitions were monitored for most of the analytes, and their intensity ratio was used for quality control. The developed methods were applied for the quantification of arsenic species in extracts of four marine reference materials. Spiking experiments revealed, especially for the early-eluting analytes on the anion exchange system, significant signal suppression by coeluting matrix constituents. Therefore, the standard addition approach was used for quantification. AsB, the major arsenic species in tuna CRM 627 and DORM-2, was accurately quantified with the combined cation anion exchange ES-SRM method.     

Isolation and identification of sialylated glycopeptides from bovine alpha1-acid glycoprotein by off-line capillary electrophoresis MALDI-TOF mass spectrometry

Sialylated glycopeptides contained in liquid chromatographic fractions of bovine alpha1-glycoprotein tryptic digests were isolated from asialo peptides using capillary electrophoresis (CE). CE effluents were deposited directly onto a metallic target and analyzed using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. This method allowed the characterization of four N-glycosylation sites in the glycoprotein, and each site was observed as a set of sialylated peptide glycoforms. Tandem mass spectrometry was used to confirm peptide sequences and glycan content in glycoforms. The CE method developed for this study resulted in a very clear separation of the sialylated from the asialo content of glycoprotein digests and proved very useful in the determination of the nature and location of sialylated glycans along the protein chain. This article is the first report describing the use of on-target CE fraction collection using a MALDI removable sample concentrator.     

Simple identification of a cross-linked hemoglobin by tandem mass spectrometry in human serum

Hemoglobin-based oxygen therapeutics are prepared by reaction of hemoglobin with cross-linking molecules and are utilized as blood substitutes. They can be used as doping agents to increase the oxygen-carrying capacity of hemoglobin. We have compared a glutaraldehyde-polymerized bovine hemoglobin (Oxyglobin, Biopure Corp.) with natural bovine hemoglobin by mass spectrometry in order to detect specific fragment ions of the cross-linked protein for further potential applications in doping control of human blood samples. HCl acid (6 N) hydrolysis was performed in parallel on both proteins. Hydrolysates were then analyzed by direct infusion electrospray mass spectrometry (ESIMS) using a triple quadrupole mass spectrometer. Confirmation and precision were obtained by LC-ESIMS(n) experiments performed on an ion trap mass spectrometer. Chromatographic and mass spectrometry data allowed detection of two potential Oxyglobin-specific ions--m/z 299 and 399--that were shown to lose a 159 u neutral fragment under collision-induced dissociation conditions. Thus, monitoring of constant neutral loss of 159 u on acid hydrolysates of human serum samples spiked with different amounts of Oxyglobin has proved to be an efficient screening method to specifically detect and identify Oxyglobin. LC-MS of the spiked serum sample hydrolysates enabled detection of Oxyglobin at a detection limit of 4 g x L(-1).     

Accumulation of arsenic and nutrients by castor bean plants grown on an As-enriched nutrient solution

Phytoextraction is a remediation technique that consists in using plants to remove contaminants from soils and water. This study evaluated arsenic (As) accumulation in Castor bean (Ricinus communis cv. Guarany) grown in nutrient solution in order to assess its phytoextraction ability. Castor bean plants were grown under greenhouse conditions in pots containing a nutrient solution amended with increasing doses of As (0, 10, 50, 100, 250, 500 and 5000 μg L⁻¹) in a completely randomized design with four replications. Shoot and roots dry matter production as well as arsenic and nutrient tissue concentrations were measured at the end of the experiment. The results showed that increasing As concentration in nutrient solution caused a decrease in shoot and root biomass but did not result in severe toxicity symptoms in castor bean growing under a range of As concentration from 0 to 5000 μg L⁻¹. The As doses tested did not affect the accumulation of nutrients by castor bean. Although castor bean did not pose characteristics of a plant suitable for commercial phytoextraction, it could be useful for revegetation of As-contaminated areas while providing an additional income by oil production.