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PubMed2003

Improvement of electron capture efficiency by resonant excitation.

A novel pulse sequence improving the efficiency for electron capture dissociation (ECD) of an unmodified Fourier transform ion cyclotron resonance (FTICR) mass spectrometer by more than an order of magnitude is presented. Commercially available FTICR instruments are usually equipped with a filament-based electron source producing an electron beam that has a rather small cross section. An ideal overlap between the rotating ion cloud and the electron beam appears to be a prerequisite for a high ECD efficiency. A reduced interception of the ion cloud and the electron beam is probably due to the contribution of the magnetron motion to the trajectory of the ions, resulting in a precession about the z-axis of the instrument. By increasing the kinetic energy and therefore increasing the cyclotron radii of the precursor ions by resonant excitation, the overlap of the rotating ion cloud with the electron beam is improved. By use of this protocol the efficiency of electron capture is substantially increased and consequently the acquisition time of ECD spectra is reduced significantly. The capability of resonant excitation of the precursor ions during the irradiation with electrons is demonstrated for standard peptides. This approach is particularly valuable for analysis and characterization of O-glycosylated peptides. In addition to amino acid sequence information, the attachment site of the labile glycan moiety is determined, and also radical-site-induced fragmentations of the glycosidic bonds are observed.

Amino Acid Sequence↗

PubMed2003

Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry.

There is an increasing need to be able to conduct quantitative lipidomics analyses as a complement to proteomics studies. The highest specificity for proteomics analysis can be obtained using methodology based on electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) coupled with liquid chromatography/tandem mass spectrometry (LC/MS/MS). For lipidomics analysis it is often necessary to be able to separate enantiomers and regioisomers. This can be very challenging when using methodology based on conventional reversed-phase chromatography. Normal-phase chromatography using chiral columns can provide dramatic improvements in the resolution of enantiomers and regioisomers. However, conventional ESI- and APCI-MS/MS has limited sensitivity, which makes it difficult to conduct studies in cell culture systems where only trace amounts of non-esterified bioactive lipids are present. The use of electron capture APCI-MS/MS overcomes this problem. Enantiomers and regioisomers of diverse bioactive lipids can be quantified using stable isotope dilution methodology coupled with normal-phase chiral chromatography and electron capture APCI-MS/MS. This methodology has allowed a lipidomics profile from rat epithelial cells maintained in culture to be delineated and allowed the effect of a non-selective lipoxygenase inhibitor to be assessed.

Animals↗

PubMed2005

Mass spectrometric detection of biotinylated peptides captured by avidin functional affinity electrophoresis.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to detect biotinylated peptides captured by avidin functional affinity electrophoresis (AFAEP). Peptide samples loaded onto AFAEP were heated with sodium dodecyl sulfate to ensure that the peptides are negatively charged, and thus migrate electrophoretically toward the cathode through the embedded avidin zone in the middle of the gel. To detect the biotinylated peptides, the band containing the avidin-biotinylated peptide complexes was excised from a 7.5% w/v native polyacrylamide gel, and biotinylated peptides were extracted with aqueous 95% v/v formamide (pH 8.2), aqueous 6 M guanidine HCl (pH 1.5), or water, at temperatures from 4 to 95 degrees C for periods from 5 min to 24 h. It was observed that all three solvents are capable of extracting biotinylated peptides and avidin from the gel, but the best results were obtained with aqueous 95% v/v formamide (pH 8.2) at 65 degrees C for 20 min. However, some AFAEP-captured biotinylated peptides are not stable and are extensively modified by formamide during extraction at too high a temperature or too long an extraction time.

Avidin↗

PubMed2005

Direct analysis of laser capture microdissected endometrial carcinoma and epithelium by matrix-assisted laser desorption/ionization mass spectrometry.

Direct analysis of laser capture microdissected malignant and normal endometrial epithelium using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (MS) was able to detect a number of proteins that are overexpressed in malignant epithelial cells. A total of 16 physiologic and malignant endometrial samples were laser capture microdissected, including four proliferative and four secretory endometria, and eight endometrioid adenocarcinomas. Two of these proteins, at 10,834 and 10,843 Da, likely correspond to calgranulin A and chaperonin 10, two proteins that had previously been identified in endometrioid adenocarcinoma in whole tissue homogenate by MS analysis. Direct analysis by MALDI-MS not only confirms that these proteins are overexpressed in endometrial carcinoma, but also localizes them to the epithelial cells, the expected cancer site.

Biomarkers, Tumor↗

PubMed2006

Comparison of the fragmentation pattern induced by collisions, laser excitation and electron capture. Influence of the initial excitation.

Collision-induced dissociation, laser-induced dissociation and electron-capture dissociation are compared on a singly and doubly protonated pentapeptide. The dissociation spectrum depends on the excitation mechanism and on the charge state of the peptide. The comparison of these results with the conformations obtained from Monte Carlo simulations suggests that the de-excitation mechanism following a laser or an electron-capture excitation is related to the initial geometry of the peptide.

Computer Simulation↗

PubMed2006

Electron capture dissociation mass spectrometry of peptide cations containing a lysine homologue: a mobile proton model for explaining the observation of b-type product ions.

Eleven doubly protonated peptides with a residue homologous to lysine were investigated by electron capture dissociation mass spectrometry (ECD-MS). Lysine homologues provide the unique opportunity to examine the ECD fragmentation behavior by allowing us to vary the length of the lysine side chain, with minimal structural change. The lysine homologue has a primary amine side chain with a length that successively decreases by one methylene (CH(2)) unit from the --CH(2)CH(2)CH(2)CH(2)NH(2) of lysine and the accompanying decrease of its proton affinities: lysine (K), 1006.5(+/-7.2) kJ/mol; ornithine (K(*)), 1001.1(+/-6.6) kJ/mol; 2,4-diaminobutanoic acid (K(**)), 975.8(+/-7.4) kJ/mol; 2,3-diaminopropanoic acid (K(***)), 950.2(+/-7.2) kJ/mol. In general, the lysine-homologous peptides exhibited overall ECD fragmentation patterns similar to that of the lysine-containing peptides in terms of the locations, abundances, and ion types of products, such as yielding c(+) and z(+.) ions as the dominant product ions. However, a close inspection of product ion mass spectra showed that ECD-MS for the alanine-rich peptides with an ornithinyl or 2,4-diaminobutanoyl residue gave rise to b ions, while the lysinyl-residue-containing peptides did not, in most cases, produce any b ions. The peptide selectivity in the generation of b(+) ions could be understood from within the framework of the mobile proton model in ECD-MS, previously proposed by Cooper (Ref. 29). The exact mass analysis of the resultant b ions reveals that these b ions are not radical species but rather the cationic species with R-CO(+) structure (or protonated oxozalone ion), that is, b(+) ions. The absence of [M+2H](+.) species in the ECD mass spectra and the selective b(+)-ion formation are evidence that the peptides underwent H-atom loss upon electron capture, and then the resulting reduced species dissociated following typical MS/MS fragmentation pathways. This explanation was further supported by extensive b(+) ions generated in the ECD of alanine-based peptides with extended conformations.

Antimicrobial Cationic Peptides↗

PubMed2002

Electron capture negative ion mass spectra of some typical matrix-assisted laser desorption/ionization matrices.

A series of seven typical matrix-assisted laser desorption/ionization (MALDI) matrices has been investigated by means of electron capture negative ion mass spectrometry (ECNI-MS). It has been shown that the most effective matrices form deprotonated negative ions predominantly in the low-energy region. Relative dissociative cross sections have been measured for all molecules under investigation. The relative integrated abundance of [M - H](-) ion formation in the series changes by four orders of magnitude. It has been shown that 2,5-DHB (gentisic acid), one of the most effective MALDI matrices, has maximal relative intensity of [M - H](-) formation at the energy approximately equal 0.8 eV. This result is in accordance with a finding of Frankevich and Zenobi [Book of Abstracts, Workshop-school "Mass spectrometry in chemical physics, bio-physics and environmental sciences", Zvenigorod, Russia, April, 25-26, 2002, p. 40] that a probable origin of negative ions in MALDI is the process of low-energy (0.5-1 eV) dissociative electron capture by matrix molecules.

Algorithms↗

PubMed1995

Scintillation proximity assay to measure binding of soluble fibronectin to antibody-captured alpha 5 beta 1 integrin.

A scintillation proximity assay (SPA) has been developed to measure binding of alpha 5 beta 1 integrin, a heterodimeric cell-surface adhesion receptor, to fibronectin. This assay utilizes an anti-beta 1 integrin monoclonal antibody to simultaneously capture alpha 5 beta 1 from a cellular lysate and couple the integrin to anti-mouse IgG antibody-coated SPA beads for detection of 125I-fibronectin binding. The assay does not require prior purification of alpha 5 beta 1 nor physical separation of bound and free 125I-fibronectin. Chinese hamster ovary cells that stably overexpress human alpha 5 integrin (CHO#7 cells) were used as a source of alpha 5 beta 1 fibronectin receptor. Using the anti-hamster beta 1 monoclonal antibody 7E2 to capture alpha 5 beta 1 from a CHO#7 cell lysate, this SPA assay allowed measurement of specific 125I-fibronectin binding as defined by displacement by the Arg-Gly-Asp containing peptide GRGDSP or the anti-human alpha 5 antibody P1D6. IC50 values for displacement of 125I-fibronectin binding by GRGDSP and the novel cyclic peptides cRGDGF, cRGEGF, and cRRETAWA were 2.6, 0.045, 3.2, and 37 microM, respectively. Specific 125I-fibronectin binding to alpha 5 beta 1 from C8161 human melanoma cells was also measured using anti-human beta 1 antibodies. This method should be generally useful to measure cell-free ligand binding to receptors that are difficult to purify.

Amino Acid Sequence↗

PubMed1996

Cloning of murine LAG-3 by magnetic bead bound homologous probes and PCR (gene-capture PCR).

In recent years PCR-based gene cloning strategies have found wide application in molecular biology, due to the power, speed, and relative simplicity of the PCR methodology. We have set up a novel PCR cloning strategy to isolate homologous genes, which is based on the capture of the cDNA sequence(s) of interest with a biotinylated probe and streptavidin-coupled magnetic beads followed by PCR amplification of the selected molecules. This method does not require sequence information on 5' and 3' regions of the cDNA of interest and permits gene isolation to be sensitive, fast, simple, and specific even when the conventional screening procedures give rise to high backgrounds. By using this technique, which we propose to call gene-capture PCR (GC-PCR) cloning, we were able to isolate the full-length murine lymphocyte activation gene 3 (LAG-3) cDNA from total RNA of activated thymocytes. The GC-PCR technique represents a powerful tool for easy isolation not only of homologous genes from related species, but also of genes sharing conserved regions of suitable length, gene variants, and gene encoding proteins where only limited knowledge of the amino acid sequence exists.

Amino Acid Sequence↗

PubMed2001

Analysis of malondialdehyde in biological matrices by capillary gas chromatography with electron-capture detection and mass spectrometry.

A gas chromatographic method is described for the quantification of free and total malondialdehyde (MDA) in biological materials. The procedure involves derivatization of the analyte with 2,4,6-trichlorophenylhydrazine, extraction with n-hexane, and separation of the cyclic derivatization product on a OV-5 gas chromatographic column. Concentration of the derivatization reagent, pH, reaction time, and temperature were investigated to determine the optimal derivatization conditions. Under these conditions, the method allows for the selective detection of free and total MDA at femtomole levels in several biological materials without any interferences. The procedure yields relative standard deviation values for the intra- and interassays in the range 3.3 and 3.9%, respectively, for the electron-capture and mass-selective (SIM mode) detection systems. Recoveries of MDA from spiked matrices reached 96%. The present method offers the advantage of the alternative use of either electron-capture or mass-selective detection. Furthermore it avoids overestimation of MDA since it employs mild conditions for sample processing and there is no need for preventing protein separation for the assessment of free MDA.

Gas Chromatography-Mass Spectrometry↗

PubMed2001

Measurement of low picomolar levels of triamcinolone acetonide in human bronchoalveolar lavage fluid by gas chromatography-electron-capture negative-ion mass spectrometry.

The intense inherent electron-capture properties of the C21 acetate derivative of triamcinolone acetonide (TAA) under methane chemical ionization mass spectrometric conditions were exploited for the development of a highly sensitive and selective gas chromatography-mass spectrometric (GC-MS) technique for measurement of levels of TAA in human bronchoalveolar lavage (BAL) fluid. After the addition of 3.0 ng of a heptadeuterated analog of TAA and varying concentrations of TAA to 2-ml aliquots of BAL fluid, the deuterium and protium forms of the steroid were extracted with diethyl ether, converted to the C21 acetate derivative, and purified via adsorptive chromatography prior to GC-MS analysis. Standard curves obtained from 2-ml aliquots of BAL fluid were linear over a wide range of concentrations of TAA from 0.0 to 24,600 pg/2-ml aliquots of BAL fluid. Levels as low as 6.0 pg/ml (13.8 pmol x L(-1)) in BAL fluid can be reliably determined in 2-ml aliquots of the biological fluid with <10% error. These findings suggest that the assay method exploiting the intense electron-capture properties of TAA is highly suitable for determination of the deposition pattern and in vivo kinetics of TAA in human airways following inhalation of the steroid.

Bronchoalveolar Lavage Fluid↗

PubMed2001

Wingless capture by Frizzled and Frizzled2 in Drosophila embryos.

A variety of factors could influence how far developmental signals spread. For example, the Patched receptor limits the range of its ligand Hedgehog. Somehow, the Frizzled2 receptor has the opposite effect on its ligand. Increasing the level of Frizzled2 stabilizes Wingless and thus extends the Wingless gradient in Drosophila wing imaginal disks. Here we ask whether Frizzled or Frizzled2 affects the spread of Wingless in Drosophila embryos. We show that in the embryonic epidermis, the combined expression of both receptors is lowest in the engrailed domain. This is because expression of Frizzled is repressed by the Engrailed transcription factor, whereas that of Frizzled2 is repressed by Wingless signaling. Receptor downregulation correlates with an early asymmetry in Wingless distribution, characterized by the loss of Wingless staining in the engrailed domain. Raising the expression of either Frizzled or Frizzled2 in this domain prevents the early disappearance of Wingless-containing vesicles. Apparently, Wingless is captured, stabilized, and quickly internalized by either receptor. As far as we can tell, captured Wingless is not passed on to further cells and does not contribute to the spread of Wingless. Receptor downregulation in the posterior compartment may contribute to dampening the signal at the time when cuticular fates are specified.

Animals↗

PubMed1996

Capture and confinement stress in white sucker exposed to bleached kraft pulp mill effluent.

This study evaluates the effects of handling and confinement stress and a 3-day recovery period on a number of biochemical parameters used to monitor exposure of fish to bleached kraft mill effluent (BKME). Plasma was collected at four times of the day from male and female white sucker subjected to four levels of handling stress during their spawning migration at a BKME and a reference site. Indicators of a general response to stress (plasma cortisol, glucose, lactate, and total protein) and of reproductive fitness (plasma testosterone, 11-ketotestosterone, and 17 beta-estradiol) were measured. With the exception of 17 beta-estradiol in females, all of the parameters measured varied with time of day and stress level. The general stress indicators ranged from being highly to marginally responsive to handling and confinement stress and were inconsistent in terms of indicating a site difference. The reproductive steroids were moderately responsive to stress and gave the most consistent site difference with testosterone and 11-ketotestosterone levels reduced in BKME-exposed fish under low levels of stress. There was limited evidence for recovery from capture, handling, and transport in the spring for plasma cortisol, lactate, and 17 beta-estradiol at the BKME site, plasma glucose at the reference site, and plasma testosterone at both sites. Fish were also more responsive to an additional acute stress on Day 1 and Day 3 of recovery compared to that on Day 0. This study emphasizes the need for standardized methods in field collections and sampling with the least amount of stress possible, and suggests that holding white sucker for 1 or 3 days does not allow them to recover from the stress of capture.

Analysis of Variance↗

PubMed2001

Ecological factors underlying the adrenocortical response to capture stress in arctic-breeding shorebirds.

Birds breeding in the Arctic must carefully balance survival and reproduction because of the often extreme environmental conditions and the very brief breeding season. Acute elevation of plasma corticosterone is one mechanism that birds apparently use to alter the balance in favor of survival at the expense of reproduction when faced with stressors such as storms, predators, or low food availability. To examine this relationship, we applied a standardized stressor, capture and handling, to four species of shorebirds (Scolopacidae) during their breeding season in the Arctic and measured the increase in corticosterone between 3 min and 30 min after capture (hereafter called the stress response). We tested two hypotheses in an effort to explain the individual variation observed in the stress response. The first hypothesis states that individuals most responsible for parental care have a lower stress response than individuals less responsible for parental care. In species with uniparental care (Pectoral Sandpiper Calidris melanotos, Red Phalarope Phalaropus fulicaria), the caregivers had a lower stress response than the opposite sex, although in the latter species the difference was not significant (P = 0.016 and P = 0.102, respectively). In a species with equal biparental care (Semipalmated Sandpiper C. pusilla), the stress response did not differ between the sexes (P = 0.99, Barrow population). In a species with unequal biparental care (Western Sandpiper C. mauri), the more parental sex (males) had a much lower stress response than the less parental sex (P = 0.002). The second hypothesis states that individuals breeding in the high Arctic have a lower stress response than individuals breeding in the low Arctic. The stress response in a low-Arctic population of Semipalmated Sandpipers (Nome) was higher than that in a high-Arctic population (Barrow, P < 0.05). Individuals at an additional high-Arctic location (Prudhoe Bay) exhibited stress responses most similar to those of the Barrow population (P > 0.05). Taken together, these results provide evidence of a mechanism that birds may use to breed in environments with a brief breeding season and under conditions that might be perceived as stressful, if not for their reduced sensitivity to potential stressors.

Adrenal Cortex↗

PubMed1995

Selection of hybrids by affinity capture (SHAC): a method for the generation of cDNAs enriched in sequences from a specific chromosome region.

We have established a method for preparing cDNA sublibraries enriched in sequences from specific chromosome regions, called selection of hybrids by affinity capture (SHAC). This procedure can be described in two stages. In the first stage, a particular chromosome region, in this study mouse chromosome 11, was microdissected, followed by PCR amplification with a universal degenerate primer. This material is referred to as the "target" DNA. In the second stage, a mouse liver cDNA library with unique linker-adapter ends, referred to as the "source" cDNA, was hybridized to the biotin-labeled target DNA prepared during the first stage. The resulting DNA duplexes were captured by streptavidin-coated magnetic beads. The cDNAs were released from their biotin-labeled target homologs by alkaline denaturation and recovered by PCR amplification. These cDNAs were referred to as the SHACcDNAs. Specificity of the SHACcDNA to chromosome 11 was verified by FISH analysis. To examine representation of the SHACcDNA, we confirmed the presence of seven genes or single-copy DNA segments known to be localized on mouse chromosome 11, using a dot blot assay. In addition, a second round of SHAC was performed to achieve even higher specificity for the resulting chromosome 11 SHACcDNA. The SHAC technology should facilitate construction of cytogenetically defined cDNA libraries and should assist in the fields of gene discovery and genome mapping.

Animals↗

PubMed1995

Isolation of murine telomere-proximal sequences by affinity capture and PCR.

We describe a method of selectively enriching for murine telomere-proximal sequences using affinity capture followed by PCR amplification. The telomeric fragments were selected from NotI-digested and lambda exonuclease-resected mouse genomic DNA by annealing to a biotinylated riboprobe containing multiple copies of the telomere repeat (TTAGGG)n. The resultant DNA-RNA hybrids were selectively retained on a matrix with covalently bound avidin. The captured DNA was then specifically released by ribonuclease action, and PCR amplification was performed using mouse repeat primers. The PCR products were cloned and used to screen a mouse genomic cosmid library, and the resultant cosmid clones were analyzed by fluorescence in situ hybridization. Ten of 70 clones analyzed gave telomere-proximal hybridization signals, indicating an at least 500-fold enrichment for telomere-proximal sequences.

Animals↗

PubMed1997

Data note system for capturing laboratory data.

The complexity of genome data limits the usefulness of traditional database management systems. The highly interconnected structure of genome data can be captured in a data representation language based on the mathematical formalism of graphs. We have tailored graphs for describing genome data and have developed a database management system, called the Data Note System, for developing small databases to capture data from genome laboratories. To simplify the use of the Data Note System, a series of tools with graphical user interfaces has been developed. The system is designed to be easy to install and use by novice database developers with a minimal amount of computer expertise. We describe the tools and present examples of their use. The system consists of a storage facility, a schema editing tool to simplify the design of small databases, and three tools for data entry and querying.

Computers↗

PubMed1999

pPAC-ResQ: A yeast-bacterial shuttle vector for capturing inserts from P1 and PAC clones by recombinogenic targeted cloning.

We have developed a method to capture inserts from P1 and P1 artificial chromosome (PAC) clones into a yeast-bacteria shuttle vector by using recombinogenic targeting. We have engineered a vector, pPAC-ResQ, a derivative of pClasper, which was previously used to capture inserts from yeast artificial chromosome clones. pPAC-ResQ contains DNA fragments flanking the inserts in P1 and PAC vectors as recombinogenic ends. When linearized pPAC-ResQ vector and P1 or PAC DNA are cotransformed into yeast, recombination between the two leads to the transfer of inserts into pPAC-ResQ. pPAC-ResQ clones thus obtained can be further modified in yeast for functional analysis and shuttled to Escherichia coli to produce large quantities of cloned DNA. This approach provides a rapid method to modify P1/PAC clones for functional analysis.

Bacteria↗