Fragmentation characteristics of permethylated oligosaccharides using a matrix-assisted laser desorption/ionization two-stage time-of-flight (TOF/TOF) tandem mass spectrometer

Matrix-assisted laser desorption/ionization two-stage time-of-flight (MALDI-TOF/TOF) tandem mass spectrometry (MS/MS) was applied to characterize permethylated oligosaccharides. Under these ionization conditions such derivatives yield intense signals corresponding to sodium-cationized molecular species. A systematic study was conducted on a series of neutral and sialylated permethylated oligosaccharides to allow rationalization of the fragmentation processes. The major fragments observed in the MALDI-TOF/TOF-MS/MS spectra result from cleavage of glycosidic bonds, preferentially at N-acetylhexosamine and sialic acid residues. The fragments originating from both the reducing and the non-reducing ends of the glycan yield information on sequence and branching. Cross-ring cleavages, which are very informative of the linkages of the monosaccharide residues constituting these oligosaccharides, and 'internal' cleavage ions which are derived from elimination of substituents from around the pyranose ring, were also observed. This extensive fragmentation was shown to be useful for the structural characterization of oligosaccharides. MALDI-TOF/TOF-MS/MS of permethylated oligosaccharides appears to be a powerful tool for carbohydrate structural analysis.     

Pedal to the Metal: The Homogeneous Catalysis of the Native Chemical Ligation Reaction

The native chemical ligation reaction of peptide thioesters with cysteinyl peptides is a pivotal chemical process in the production of native or modified peptides and proteins, and well beyond in the preparation of various biomolecule analogs and materials. To benefit from this reaction at its fullest and to access all the possible applications, the experimentalist needs to know the factors affecting its rate and how to control it. This concept article presents the fundamental principles underlying the rate of the native chemical ligation and its homogeneous catalysis by nucleophiles. It has been prepared to serve as a quick guide in the search for an appropriate catalyst.     

Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view

The proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the mitochondrial rRNAs and a few tRNAs, we performed a comparative study on the 143B cell line and on its Rho-0 counterpart, i.e., devoid of mitochondrial DNA. Quantitative differences were found, of course in the respiratory complexes subunits, but also in the mitochondrial translation apparatus, mainly mitochondrial ribosomal proteins, and in the ion and protein import system, i.e., including membrane proteins. Various mitochondrial metabolic processes were also altered, especially electron transfer proteins and some dehydrogenases, but quite often on a few proteins for each pathway. This study also showed variations in some hypothetical or poorly characterized proteins, suggesting a mitochondrial localization for these proteins. Examples include a stomatin-like protein and a protein sharing homologies with bacterial proteins implicated in tyrosine catabolism. Proteins involved in apoptosis control are also found modulated in Rho-0 mitochondria.     

Producing SI-traceable reference values for Cd, Cr and Pb amount contents in polyethylene samples from the Polymer Elemental Reference Material (PERM) project using isotope dilution mass spectrometry

 The present paper describes the certification of the amount content of Cd, Cr and Pb in two different polyethylene materials within the third phase of the Polyethylene Elemental Reference Material (PERM) project. The analytical procedure to establish the reference values for Cd, Cr and Pb amount contents in these materials is based on isotope dilution mass spectrometry used as a primary method of measurement. Cd and Pb were measured with inductively coupled plasma-mass spectrometry and Cr with positive thermal ionization-mass spectrometry. The decomposition of the polymer matrix was carried out using a high pressure asher. Reference values for amount content, traceable to the SI-system, have been obtained for these three elements in both of the polyethylene samples of PERM. For each of the certified amount content values an uncertainty budget was calculated using the method of propagation of uncertainties according to ISO and EURACHEM guidelines. The measurement procedures, as well as the uncertainty calculations, are described for all three elements. In order to keep the whole certification process as transparent as possible, the preparations of various reagents and materials as well as the sample treatment and blending are described in detail. The mass spectrometry measurements and the data treatment are also explained carefully. The various sources of uncertainty present in the procedure are displayed in the uncertainty budgets. The obtained combined uncertainties for the amount content values were less than 2% relative (k=1) for all investigated elements. The amount contents were in the μmol/kg range, corresponding to mg/kg levels. Received: 21 October 1999 / Accepted: 29 January 2000     

Development of an ICP-IDMS method for accurate routine analyses of toxic heavy metals in polyolefins and comparison with results by TI-IDMS

An inductively coupled plasma isotope dilution mass spectrometric (ICP-IDMS) method was developed as a suitable method – with respect to its sensitivity, precision, accuracy, and time-consumption – for the analysis of toxic heavy metal traces (Pb, Cd, Cr, and Hg) in polyolefins. Results for Pb, Cd, and Cr were compared with those obtained by thermal ionization isotope dilution mass spectrometry (TI-IDMS), which was used as a reference method. Because of its high first ionization potential and its high volatility mercury could not be determined by TI-IDMS. A multi-element spike solution, containing isotopically enriched ²⁰⁶Pb, ¹¹⁶Cd, ⁵³Cr, and ²⁰¹Hg, was used for the isotope dilution step. Decomposition of the polyolefin samples was carried out with concentrated HNO₃ at temperatures of about 300?°C in a high pressure asher (HPA). This procedure decomposes polyolefins completely and allows isotopic equilibration between sample and spike isotopes. Detection limits of 16 ng/g, 5 ng/g, 164 ng/g, and 9 ng/g were obtained for Pb, Cd, Cr, and Hg by ICP-IDMS using only sample weights of 0.25 g. In different commercially available polyethylene samples heavy metal concentrations in the range of < 5 ng/g to 4 × 10³ ng/g were analyzed. Both mass spectrometric methods were applied within the EU project “Polymeric Elemental Reference Material (PERM)” for the certification of two polyethylene reference materials. The ICP-IDMS results agreed very well with those of TI-IDMS which demonstrates the accuracy of the ICP-IDMS method also suitable for routine analyses.     

Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.     

Bromide/bromate speciation by NTI-IDMS and ICP-MS coupled with ion exchange chromatography

 Two different mass spectrometric methods, negative thermal ionization isotope dilution mass spectrometry (NTI-IDMS) and inductively coupled plasma mass spectrometry (ICP-MS), off-line and on-line coupled with anion exchange chromatography, have been developed for simultaneous bromide and bromate determinations in water samples. The detection limits of these methods are in the range of 0.03–0.09 μg/L using a 50 mL sample.The results are independent of the content of other anions, which could be demonstrated by the analyses of six mineral waters containing chloride and sulfate of up to 160 mg/L and 1500 mg/L, respectively. Bromide has been analyzed by the NTI-IDMS method in the range of 10–500 μg/L and bromate in the range of 1–50 μg/L with relative standard deviations of 0.3–1.2% and 0.4–6%. Quantification for the ICP-MS method was carried out by the standard addition technique, which resulted in relative standard deviations of 5.5% for bromide at the 500 μg/L level and of 13% for bromate at the level of about 3 μg/L. These results are compared with those described in the literature for ion chromatographic (IC) and other methods and those obtained in this work by IC using UV detection, which allows high concentrations of chloride in the bromate fraction. The detection limits of this IC method are 6 μg/L for bromide and 30 μg/L for bromate. NTI-IDMS and ICP-MS therefore fit the recommendations of the European Union (detection limit<2.5 μg/L; precision and accuracy better than 25% at the 10 μg/L level) for methods analyzing the carcinogenic bromate much better than IC and other methods applied up to now. As a definitive but time consuming method, NTI-IDMS is preferably applicable as a calibration technique, whereas ICP-MS, with relatively short analysis times, due to on-line coupling with chromatography, can be used as a sensitive and powerful routine method for trace bromide and bromate species in water samples. Received: 5 July 1996/Accepted: 7 August 1996     

Detection and structural features of the βB2‐B3‐crystallin heterodimer by radical probe mass spectrometry (RP‐MS)

The predilection of the β‐crystallin B2 subunit to interact with the βB3 subunit rather than self associate is evident by the detection of the βB2‐B3‐crystallin heterodimer by native gel electrophoresis and electrospray ionisation time‐of‐flight (ESI‐TOF) mass spectrometry under non denaturing conditions. The complex has been detected for the first time and its molecular mass is measured to be 47 450 ± 1 Da. Radical probe mass spectrometry (RP‐MS) was subsequently applied to investigate the nature of the heterodimer through the limited oxidation of the subunits in the complex. Two peptide segments of the βB2 subunit and six of the βB3 subunit were found to oxidise, with far greater oxidation observed within the βB3 versus the βB2 subunit. This, and the observation that the oxidation data of βB2 subunit is inconsistent with the structure of the βB2 monomer, demonstrates that the protection of βB2 is conferred by its association with βB3 subunit within the heterodimer where only the residues of, and towards, its N‐terminal domain remain exposed to solvent. The results suggest that the βB2 subunit adopts a more compacted form than in its monomeric form in order for much of its structure to be enveloped by the βB3 subunit within the heterodimer. Copyright © 2009 John Wiley & Sons, Ltd.