Lipopeptides from the Banyan Endophyte, Bacillus subtilis K1: Mass Spectrometric Characterization of a Library of Fengycins

Mass spectrometric analysis of a banyan endophyte, Bacillus subtilis K1, extract showing broad spectrum antifungal activity revealed a complex mixture of lipopeptides, iturins, surfactins, and fengycins. Fractionation by reversed-phase high performance liquid chromatography (HPLC) facilitated a detailed analysis of fengycin microheterogeneity. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric studies permitted the identification of several new fengycin variants. Four major sites of heterogeneity are identified: (1) N-terminus beta-hydroxy fatty acid moiety, where chain length variation and the presence of unsaturation occur, (2) position 6 (Ala/Val/Ile/Leu), (3) position 10 (Val/Ile) within the macrocyclic ring, and (4) Gln to Glu replacement at position 8, resulting in fengycin variants that differ in mass by 1 Da. Diagnostic fragment ions provide a quick method for localizing the sites of variation in the macrocycle or the linear segment. Subsequent establishment of the sequences is achieved by MS/MS analysis of linear fengycin species produced by hydrolysis of the macrocyclic lactone. Unsaturation in the fatty acid chain and the presence of linear precursors in the B. subtilis K1 extract are also established by mass spectrometry. The anomalous distribution of intensities within isotopic multiplets is a diagnostic for Gln/Glu replacements. High resolution mass spectrometry facilitates the identification of fengycin species differing by 1 Da by localizing the variable position (Gln(8)/Glu(8)) in the fengycin variants.

Precision and long-term stability of clumped-isotope analysis of CO2 using a small-sector isotope ratio mass spectrometer

RATIONALE The ratio of the measured abundance of 13C18O bonding CO2 to its stochastic abundance, prescribed by the delta 13C and delta 18O values from a carbonate mineral, is sensitive to its growth temperature. Recently, clumped-isotope thermometry, which uses this ratio, has been adopted as a new tool to elucidate paleotemperatures quantitatively. METHODS Clumped isotopes in CO2 were measured with a small-sector isotope ratio mass spectrometer. CO2 samples digested from several kinds of calcium carbonates by phosphoric acid at 25 degrees C were purified using both cryogenic and gas-chromatographic separations, and their isotopic composition (delta 13C, delta 18O, Delta 47, Delta 48 and Delta 49 values) were then determined using a dual-inlet Delta XP mass spectrometer. RESULTS The internal precisions of the single gas Delta 47 measurements were 0.005 and 0.02 parts per thousand (1 SE) for the optimum and the routine analytical conditions, respectively, which are comparable with those obtained using a MAT 253 mass spectrometer. The long-term variations in the Delta 47 values for the in-house working standard and the heated CO2 gases since 2007 were close to the routine, single gas uncertainty while showing seasonal-like periodicities with a decreasing trend. Unlike the MAT 253, the Delta XP did not show any significant relationship between the Delta 47 and delta 47 values. CONCLUSIONS The Delta XP gave results that were approximately as precise as those of the MAT 253 for clumped-isotope analysis. The temporal stability of the Delta XP seemed to be lower, although an advantage of the Delta XP was that no dependency of delta 47 on Delta 47 was found. Copyright (c) 2012 John Wiley & Sons, Ltd.

A modified auxiliary excitation signal for achieving unidirectional ion ejection in quadrupole ion trap mass spectrometers operating in the resonance ejection mode

This paper proposes a technique to cause unidirectional ion ejection in a quadrupole ion trap mass spectrometer operated in the resonance ejection mode. In this technique a modified auxiliary dipolar excitation signal is applied to the endcap electrodes. This modified signal is a linear combination of two signals. The first signal is the nominal dipolar excitation signal which is applied across the endcap electrodes and the second signal is the second harmonic of the first signal, the amplitude of the second harmonic being larger than that of the fundamental. We have investigated the effect of the following parameters on achieving unidirectional ion ejection: primary signal amplitude, ratio of amplitude of second harmonic to that of primary signal amplitude, different operating points, different scan rates, different mass to charge ratios and different damping constants. In all these simulations unidirectional ejection of destabilized ions has been successfully achieved. (C) 2015 Elsevier B.V. All rights reserved.

Differential binding of ppGpp and pppGpp to E-coli RNA polymerase: photo-labeling and mass spectral studies

(p) ppGpp, a secondary messenger, is induced under stress and shows pleiotropic response. It binds to RNA polymerase and regulates transcription in Escherichia coli. More than 25 years have passed since the first discovery was made on the direct interaction of ppGpp with E. coli RNA polymerase. Several lines of evidence suggest different modes of ppGpp binding to the enzyme. Earlier cross-linking experiments suggested that the beta-subunit of RNA polymerase is the preferred site for ppGpp, whereas recent crystallographic studies pinpoint the interface of beta'/omega-subunits as the site of action. With an aim to validate the binding domain and to follow whether tetra-and pentaphosphate guanosines have different location on RNA polymerase, this work was initiated. RNA polymerase was photo-labeled with 8-azido-ppGpp/8-azido-pppGpp, and the product was digested with trypsin and subjected to mass spectrometry analysis. We observed three new peptides in the trypsin digest of the RNA polymerase labeled with 8-azido-ppGpp, of which two peptides correspond to the same pocket on beta'-subunit as predicted by X-ray structural analysis, whereas the third peptide was mapped on the beta-subunit. In the case of 8-azido-pppGpp-labeled RNA polymerase, we have found only one cross-linked peptide from the beta'-subunit. However, we were unable to identify any binding site of pppGpp on the beta-subunit. Interestingly, we observed that pppGpp at high concentration competes out ppGpp bound to RNA polymerase more efficiently, whereas ppGpp cannot titrate out pppGpp. The competition between tetraphosphate guanosine and pentaphosphate guanosine for E. coli RNA polymerase was followed by gel-based assay as well as by a new method known as DRaCALA assay.

Mass spectrometric analysis of dimer-disrupting mutations in Plasmodium triosephosphate isomerase

Electrospray ionization mass spectrometry (ESI MS) under nanospray conditions has been used to examine the effects of mutation at two key dimer interface residues, Gln (Q) 64 and Thr (T) 75, in Plasmodium falciparum triosephosphate isomerase. Both residues participate in an intricate network of intra- and intersubunit hydrogen bonds. The gas phase distributions of dimeric and monomeric protein species have been examined for the wild type enzyme (TWT) and three mutants, Q64N, Q64E, and 175S, under a wide range of collision energies (40-160 eV). The results established the order of dimer stability as TWT > T75S > Q64E similar to Q64N. The mutational effects on dimer stability are in good agreement with the previously reported estimates, based on the concentration dependence of enzyme activity. Additional experiments in solution, using inhibition of activity by a synthetic dimer interface peptide, further support the broad agreement between gas phase and solution studies. (C) 2016 Elsevier Inc. All rights reserved.

A pilot experiment for mass measurement at CSRe

A pilot experiment of mass measurement was performed at CSRe with the method of isochronous mass spectrometry. The secondary fragments produced via RIBLL2 with the primary beam of 400 MeV/u, Ar-36 delivered by CSRm were injected into CSRe. The revolution periods of the stored ions, which depend on the mass-to-charge ratios of the stored ions, were measured with a time-of-flight detector system. The results show that the mass resolution around 8 x 10(-6) for Delta m/m is achieved.

DIRECT MASS MEASUREMENTS OF EXOTIC NUCLEI IN STORAGE RINGS

Mass measurements of exotic nuclei is a fast, developing field which is essential for basic nuclear physics and a wide range of applications. The method of storage ring mass spectrometry has many advantages: (1) a large amount of nuclides can be simultaneously measured; (2) very short-lived (T-1/2 greater than or similar to 50 mu s) and very rare species (yields down to single ions) can be accessed; (3) nuclides in several atomic charge states can be investigated, (4) half-life measurements can be performed with time-resolved mass spectrometry. In this contribution we concentrate on some recent achievements and future perspectives of the storage ring mass spectrometry.

A high performance Time-of-Flight detector applied to isochronous mass measurement at CSRe

A high performance Time-of-Flight detector has been designed and constructed for isochronous mass spectrometry at the experimental Cooler Storage Ring (CSRe) The detector has been successfully used in an experiment to measure the masses of the N approximate to Z approximate to 33 nuclides near the proton drip-line Of particular interest is the mass of As-65 A maximum detection efficiency of 70% and a time resolution of 118 +/- 8 Ps (FWHM) have been achieved in the experiment The dependence of detection efficiency and signal average pulse height (APH) on atomic number Z has been studied The potential of APH for Z identification has been discussed (C) 2010 Elsevier B V All rights reserved

Secondary electron time detector for mass measurements at CSRe

The Isochronous Mass Spectrometry is a high accurate mass spectrometer. A secondary electrons time detector has been developed and used for mass measurements. Secondary electrons from a thin carbon foil are accelerated by ail electric field and deflected 180 degrees by a magnetic field onto a micro-channel plate. The time detector has been tested with alpha particles and a time resolution of 197 ps (FWHM) was obtained in the laboratory. A mass resolution around 8 x 10(-6) For Delta m/m was achieved by using this time detector in a pilot mass measurement experiment.

Calibration of an audio-frequency ion trap mass spectrometer

A method for calibration of an audio-frequency (AF) ion trap mass spectrometer is described. The method is proposed to surmount the obstacle that there is a lack of a proper calibrant for mass spectrometers in the mass-to-charge ratio (m/z) range of 10(6) to 10(10). To calibrate such mass spectra, we determine the point of ejection, q(eject), on the stability diagram of the ion trap operated in a mass-selective axial instability mode. This is accomplished by measuring the radial secular frequencies (and therefore, the m/z value) of a single trapped particle using a light scattering method, followed by monitoring the action of particle ejection in real time to obtain the q(eject). A delayed ejection with q(eject) = 0.949 +/- 0.004 is found at a trap driving frequency of Ohm/2pi = 200-600Hz. Theoretical analysis for the origin of the delayed ejection indicates that the delay is predominantly resulted from the existence of multipole components in the fields due to trap imperfections. Inclusion of -3% of the octopole with respect to the basic quadrupole field can satisfactorily account for our observations. An m/z accuracy approaching 0.1% is attainable after proper calibration of the AF ion trap mass spectrometer. (Int J Mass Spectrom 214 (2002) 63-73) (C) 2002 Elsevier Science B.V. All rights reserved.

High resolution mass spectrometric alveolar proteomics: Identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients

In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micro preparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products.