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  • 1
    Keywords: PEPTIDE ; Germany ; PROTEIN ; COMPLEXES ; IONS ; SEQUENCE ; SIGNAL ; IDENTIFICATION ; mass spectrometry ; MASS-SPECTROMETRY ; PEPTIDES ; CALCIUM ; GAS-PHASE ; RE ; RESIDUES ; GRADE ; ASPARTIC-ACID ; LEVEL ; CALCIUM-BINDING ; VIEW ; SIGNALS ; FRAGMENT ; STOICHIOMETRY ; ACID-RESIDUES ; GLYCOCLUSTERS ; LITHIATED ADDUCTS ; METAL-ION
    Abstract: In an analysis of a combined chymotrypsin/AspN digest of galectin-3 by positive ion nano-electrospray ionisation mass spectrometry (nanoESI-MS) several peptides were observed which showed metal adduct ions as their most abundant ion signals. The most prominent adduct ions were observed at m/z values corresponding to [M+40](2+), [M+41](3+), and [M+42](4+) ions. Detailed investigation of the [M+40](2+) ion of the peptide GAPAGPLIVPY showed that it was not, as originally expected, a [M+H+K-39](2+) adduct ion but had the.composition [M+Ca-40](2+). This was verified by several approaches: W nanoESI-MS/MS of the [M+Ca](2+) adduct ions resulted in the virtually exclusive formation of doubly charged fragment ions; (ii) mass determination by quadrupole time-of-flight (QTOF)-MS provided a preliminary identification; and (iii) accurate mass measurement using nanoESI Fourier transform ion cyclotron resonance (FTICR)-MS at a mass resolving power of 500000 allowed the specific detection and identification of the isobaric ion pairs [M+Ca-40](2+)/ [M+H+K-39](2+) and [M+Mg-24](2+)/[M+H+(23) Na](2+). All peptides in the chymotryptic galectin-3 digest without a basic residue (K or R) showed addition of calcium as the most prominent ionisation principle. A further common feature of these nonbasic peptides was the presence of several proline residues, which is assumed to be a factor promoting the intense addition of calcium. It was observed that the common trace levels of sodium and calcium in analytical grade solvents (about 1-10 mu M) are sufficient to generate the [M+H+Na-23](2+) and [M+Ca-40](2+) ions as the most prominent species of the peptide GAPAGPLIVPY. We conclude that the sequence motifs P-XX-P and P-XXX-P favour the solvation of alkaline earth ions in ESI-MS. In view of the successful detection of physiological Ca/ protein interactions by ESI-MS, this finding may point to a solvation of Ca2+ by galectin in solution. The findings open new routes of research in the study of metal/protein and metal/peptide interactions. Copyright (c) 2006 John Wiley & Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 16841364
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  • 2
    Abstract: RATIONALE: A bottleneck in metabolic profiling of complex biological extracts is confident, non-supervised annotation of ideally all contained, chemically highly diverse small molecules. Recent computational strategies combining sum formula prediction with in silico fragmentation achieve confident de novo annotation, once the correct neutral mass of a compound is known. Current software solutions for automated adduct ion assignment, however, are either publicly unavailable or have been validated against only few experimental electrospray ionization (ESI) mass spectra. METHODS: We here present findMAIN (find Main Adduct IoN), a new heuristic approach for interpreting ESI mass spectra. findMAIN scores MS1 spectra based on explained intensity, mass accuracy and isotope charge agreement of adducts and related ionization products and annotates peaks of the (de)protonated molecule and adduct ions. The approach was validated against 1141 ESI positive mode spectra of chemically diverse standard compounds acquired on different high-resolution mass spectrometric instruments (Orbitrap and time-of-flight). Robustness against impure spectra was evaluated. RESULTS: Correct adduct ion assignment was achieved for up to 83% of the spectra. Performance was independent of compound class and mass spectrometric platform. The algorithm proved highly tolerant against spectral contamination as demonstrated exemplarily for co-eluting compounds as well as systematically by pairwise mixing of spectra. When used in conjunction with MS-FINDER, a state-of-the-art sum formula tool, correct sum formulas were obtained for 77% of spectra. It outperformed both 'brute force' approaches and current state-of-the-art annotation packages tested as potential alternatives. Limitations of the heuristic pertained to poorly ionizing compounds and cationic compounds forming [M]+ ions. CONCLUSIONS: A new, validated approach for interpreting ESI mass spectra is presented, filling a gap in the nontargeted metabolomics workflow. It is freely available in the latest version of R package InterpretMSSpectrum.
    Type of Publication: Journal article published
    PubMed ID: 28499062
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  • 3
    Keywords: AB-INITIO ; ENERGIES ; SPECTRA ; PATHWAYS ; SUPPORT ; COMPLEX ; COMPLEXES ; MECHANISM ; primary ; IONS ; SIGNAL ; PROTON ; FORM ; ENERGY ; COLLISION-INDUCED DISSOCIATION ; FRAGMENTS ; AFFINITY ; ENERGETICS ; PROTONATED PEPTIDES ; RRKM ; ELIMINATION ; STATES ; BOND ; IONIZATION MASS-SPECTROMETRY ; MASSES ; IMMONIUM IONS
    Abstract: Tandem mass spectrometric experiments have been carried out on the protonated amides H-Gly-Ala-NH2, H-Ala-Gly-NH2, H-Ala-Val-NH2, H-Val-Ala-pNA, H-Leu-Phe-NH2, H-Phe-Leu-NH2, H-Phe-Tyr-NH2 and H-Tyr-Phe-NH2 with particular emphasis on the fragmentation of the isomeric a(2) ions derived therefrom. Primary fragmentation reactions of the protonated amides involve formation of the y(1)" and b(2) ions with further fragmentation of the b(2) ion to form the a(2) ion which fragments to form iminium ions. Collision-induced dissociation studies of the mass-selected a(2) ions were carried out. For the Gly-Ala, Ala-Gly and Val-Ala a(2) ions, weak signals were observed corresponding to loss of CO from the a(2) ion. With the exception of the Gly-Ala, Ala-Gly and Val-Ala a(2) ions, both possible iminium ions (a(1) and the internal iminium ion) are observed with the most abundant being that formed by proton attachment to the imine of higher proton affinity. The results provide strong support for the recently proposed (El Aribi et al. J. Am. Chem. Soc. 2003; 125: 9229) mechanism of fragmentation of a(2) ions which involves elimination of CO from the a(2) ion to form a proton-bound complex of two imines. Based on this mechanism ab initio calculations of the total energies of the a(2) ions and the transition states for fragmentation have been carried out giving the energy barrier for fragmentation of each a(2) ion. The experimental results are interpreted in terms of these energetics data, unimolecular rate constants calculated by using the RRKM theory, and the imine proton affinities. Copyright (C) 2004 John Wiley Sons, Ltd
    Type of Publication: Journal article published
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  • 4
    Keywords: OPTIMIZATION ; Germany ; human ; RISK ; SAMPLE ; SAMPLES ; TISSUE ; COMPLEX ; COMPLEXES ; REDUCTION ; RISK-FACTORS ; BIOMARKERS ; QUANTITATION ; SUSCEPTIBILITY ; METABOLITES ; SPECTROSCOPY ; BREAST-CANCER ; FORM ; NUMBER ; risk factors ; GAS ; MASS-SPECTROMETRY ; PURIFICATION ; INITIATION ; ESTRADIOL ; LACKING ; METABOLITE ; MASSES ; PERFORMANCE LIQUID-CHROMATOGRAPHY ; CHEMISTRY ; RE ; monitoring ; ESTROGEN ; phytoestrogens ; Male ; RISK-FACTOR ; IMPROVEMENT ; enzymatic ; ELECTROSPRAY-IONIZATION
    Abstract: A gas chromatography/mass spectrometry (GC/MS) method for the simultaneous quantitation of ten estrogen metabolites in human urine was optimized. The method consists of initial enzymatic hydrolysis of the estrogen conjugates using beta-glucuronidase followed by solid-phase extraction (SPE) on Sep-pak C18 columns and further sample purification by ion-exchange chromatography on QAE-Sephadex cartridges in the acetate form. QAE-Sephadex cartridges in the borate form were used to separate estrogens into two fractions: one fraction containing estrogens lacking vicinal cis-hydroxyls (Fr 1) and another containing estrogens possessing vicinal cis-hydroxyls (catecholestrogens; Fr 2). Finally, following O-trimethylsilyl ether derivatization, the estrogens were analyzed by GC/MS in the selected ion monitoring mode. Estrogens were quantitated using deuterated internal standards, which were added to the samples at the initiation of the work-up procedures. After addition to estrogen-low male human samples the standards showed good chromatographic linear response and reproducibility. A reduction in the number of steps and improvements in the robustness of the work-up procedures were achieved. The modified method described is less complex, amenable to use with commercially available SPE columns and fulfils all the reliability criteria, resulting in highly specific and accurate results. Copyright (C) 2007 John Wiley & Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 17569095
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  • 5
    Keywords: PEPTIDE ; COMBINATION ; Germany ; SITES ; PROTEINS ; ACCURACY ; PHOSPHORYLATION ; ACID ; IDENTIFICATION ; mass spectrometry ; TANDEM MASS-SPECTROMETRY ; MASS-SPECTROMETRY ; TIME-OF-FLIGHT ; PEPTIDES ; STATES ; phosphoproteins ; MASSES ; molecular ; RE ; RESIDUES ; INTERFERENCE ; SODIUM ; CHARGE
    Abstract: Formation of S-carbamidomethylmethionine (camMet) occurs as a side reaction during cysteine alkylation with iodoacetamide (IAA). In collision-induced dissociation, peptides with camMet show an abundant neutral loss of 2-(methylthio)acetamide (C3H7NOS=105.025 Da) at moderate collision offset values which are similar to those optimal for loss of phosphoric acid (H3PO4 = 97.977 Da). Neutral loss analysis is used for spotting of phosphopeptides which contain phosphoserine (pSer) or phosphothreonine (pThr) residues. In the case where precursor ions cannot be accurately assigned in the survey spectrum (e.g. due to low ion abundance or signal overlap), the mass accuracy of a neutral loss tandem mass spectrometry (MS/MS) analysis depends on the precursor ion isolation window. For the charge states 2+, 3+ or 4+, a typical 3.5 Da precursor isolation window results in neutral loss windows of 7, 10.5 or 14 Da, respectively. Consequently, neutral loss of 105 Da from alkylated methionine residues can mimic the phosphoserine/phosphothreonine-specific neutral loss of 98 Da. In the evaluation of quadrupole time-of-flight (QTOF) parent ion scan data for neutral loss of H3PO4, this interference was frequently observed. It is illustrated in this study using the analysis of ovalbumin phosphorylation as an example. The +80 Da molecular weight shift connected with phosphorylation at serine or threonine may also be mimicked by carbamidomethylation of methionine through a combination with sodium adduction (+57 Da+22 Da = +79 Da). For highly sensitive neutral loss analysis of serine and threonine phosphorylation, careful data inspection is recommended if reduction and alkylation by IAA is employed. Copyright (c) 2005 John Wiley & Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 15912474
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  • 6
    Keywords: CANCER ; Germany ; RISK ; EFFICIENCY ; COMPONENTS ; RISK-FACTORS ; INTERVENTION ; ACID ; ACIDS ; IDENTIFICATION ; prevention ; colorectal cancer ; risk factors ; COLORECTAL-CANCER ; COUNTRIES ; mass spectrometry ; MASS-SPECTROMETRY ; ethanol ; CALCIUM ; antioxidants ; LIGNANS ; OLIVE OIL ; phenolic compounds ; DENMARK ; PHENOLIC-COMPOUNDS ; MATRIX ; SUBSET ; RE ; EXTRACTION ; SUPPLEMENTATION ; RECOVERY ; EUROPEAN COUNTRIES ; RISK-FACTOR ; RELEVANCE ; CAPILLARIES ; MS/MS ; ORGANIC-SOLVENTS ; CONTAMINATION
    Abstract: Very few relevant methods have been described for the detection and quantitation of phenolic compounds in faecal matrix. Extraction with conventional organic solvents such as chloroform/methanol (2:1, Folch reagent), methanol and ethanol (72%) showed high extraction efficiency for lipids and also gave good recovery of the major phenolic compounds present in the matrix. However, in comparison with a newly developed phosphate buffer method, the yield of minor phenolics was negligible when detected by these conventional methods. Conventional methods also lead to contamination of the ion source of the mass spectrometer and rapid deterioration of column performance mostly due to the high concentration of lipids. However, if the faecal matrix is initially extracted with phosphate buffer, and the extract acidified and re-extracted with diethyl ether, the range and yield of phenolic compounds are enhanced and the problem of lipid contamination is substantially alleviated. Following pilot studies and optimisation of the procedure, individual phenolic compounds (n = 29) were identified by nano-electrospray ionisation mass spectrometry (nano-ESI-MS), nano-ESI-tandem mass spectrometry (MS/MS) and gas chromatography/mass spectrometry (GC/EI-MS) and quantitated (n = 27) by GC/MS in subsets (n = 5) of faecal samples, collected during the European Agency for Cancer Prevention calcium/fibre intervention study from four European countries (Italy, Germany, Spain and Denmark). A range of phenolic compounds (mainly acids) was detected, dominated by phenylacetic, benzoic, phenylpropionic and m-hydroxyphenylpropionic acids, representing on average 9.91 (93%), 8.25 (92%), 9.45 (95%) and 11.05 (98%) mM in the Italian, German, Spanish and Danish samples, respectively. The new method should enable large epidemiologic, case-control and intervention studies on the relevance of phenolic antioxidants in the aetiology of colorectal cancer to be conducted in the future. Copyright (c) 2006 John Wiley & Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 16986210
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Type of Medium: Electronic Resource
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