| 1. |
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| 2. |
- Nilsson, Carol L, et al.
(författare)
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Characterization of the P13 membrane protein of Borrelia burgdorferi by mass spectrometry.
- 2002
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Ingår i: Journal of the American Society for Mass Spectrometry. - 1044-0305 .- 1879-1123. ; 13:4, s. 295-299
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Tidskriftsartikel (refereegranskat)abstract
- Borrelia burgdorferi sensu lato is a tick-borne pathogen that causes Lyme disease. The characterization of membrane proteins from this and other pathogens may yield a better understanding of the mechanisms of infection and information useful for vaccine design. Characterization of the highly hydrophobic Borrelia outer membrane component P13 from a mutant (OspA- OspB- OspC- and OspD-) strain was undertaken by use of a combination of mass spectrometric methods. In a previous investigation, an electrospray ionization (ESI) mass spectrum of the intact protein provided an average molecular weight that was 20 Da lower than the predicted molecular weight. The mass deviation could be explained by a modification of the N-terminus of the protein such as pyroglutamylation (-17 Da) in combination with the experimental error of measurement, however more information was required. New structural information for this membrane protein was provided by peptide mapping with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) and sequencing with ESI-quadrupole-TOF tandem MS.
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| 3. |
- Palmblad, Magnus, et al.
(författare)
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Automatic Analysis of Hydrogen/Deuterium Exchange Mass Spectra of Peptides and Proteins using Calculations of Isotopic Distributions
- 2001
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Ingår i: Journal of the American Society for Mass Spectrometry. - 1044-0305 .- 1879-1123. ; 12:11, s. 1153-1162
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Tidskriftsartikel (refereegranskat)abstract
- High mass-resolving power has been shown to be useful for studying the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange. A computer algorithm was developed that automatically identifies peptides and their extent of deuterium incorporation from H/D exchange mass spectra of enzymatic digests or fragment ions produced by collisionally induced dissociation (CID) or electron capture dissociation (ECD). The computer algorithm compares measured and calculated isotopic distributions and uses a fast calculation of isotopic distributions using the fast Fourier transform (FFT). The algorithm facilitates rapid and automated analysis of H/D exchange mass spectra suitable for high-throughput approaches to the study of peptide and protein structures. The algorithm also makes the identification independent on comparisons with undeuterated control samples. The applicability of the algorithm was demonstrated on simulated isotopic distributions as well as on experimental data, such as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin peptic digests, and CID and ECD spectra of substance P.
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| 4. |
- Zubarev, Roman A., et al.
(författare)
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Isotope depletion of large biomolecules : Implications for molecular mass measurements
- 1998
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Ingår i: Journal of the American Society for Mass Spectrometry. - 1044-0305 .- 1879-1123. ; 9:2, s. 149-156
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Isotope depletion (or enrichment) of large biomolecules is a procedure already used in high resolution Fourier transform ion cyclotron resonance mass spectrometry for improving the reliability and accuracy of biomolecular mass characterization. In this work, effects of isotope depletion on a number of mass spectrometric parameters are systematically studied. Implementation of the isotope depletion techniques in conjunction with lower resolution mass analyzers is discussed as well. We investigate theoretically the position of the centroid of the isotopic mass distributions (centroid mass) and the shift between the monoisotopic and the centroid masses of biopolymers as a function of the isotope abundance (e.g., 12C:13C ratio). The behaviour of other additive mass parameters, like the ratio between the monoisotopic and the first isotopic peak, is also discussed. We address by computer simulations the effects of different instrumental parameters like mass resolution and ion statistics as a function of isotope abundances and from there the achievable mass accuracy for high-mass biopolymers. We assess some of the practical issues of the isotope depletion technique, viz., to what degree and with what accuracy the depletion procedure should be performed for achieving the desired mass accuracy.
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| 5. |
- Abrahamsson, Dimitri, et al.
(författare)
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In Silico Structure Predictions for Non-targeted Analysis : From Physicochemical Properties to Molecular Structures
- 2022
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 33:7, s. 1134-1147
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Tidskriftsartikel (refereegranskat)abstract
- While important advances have been made in high-resolution mass spectrometry (HRMS) and its applications in non-targeted analysis (NTA), the number of identified compounds in biological and environmental samples often does not exceed 5% of the detected chemical features. Our aim was to develop a computational pipeline that leverages data from HRMS but also incorporates physicochemical properties (equilibrium partition ratios between organic solvents and water; Ksolvent–water) and can propose molecular structures for detected chemical features. As these physicochemical properties are often sufficiently different across isomers, when put together, they can form a unique profile for each isomer, which we describe as the “physicochemical fingerprint”. In our study, we used a comprehensive database of compounds that have been previously reported in human blood and collected their Ksolvent–water values for 129 partitioning systems. We used RDKit to calculate the number of RDKit fragments and the number of RDKit bits per molecule. We then developed and trained an artificial neural network, which used as an input the physicochemical fingerprint of a chemical feature and predicted the number and types of RDKit fragments and RDKit bits present in that structure. These were then used to search the database and propose chemical structures. The average success rate of predicting the right chemical structure ranged from 60 to 86% for the training set and from 48 to 81% for the testing set. These observations suggest that physicochemical fingerprints can assist in the identification of compounds with NTA and substantially improve the number of identified compounds.
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| 6. |
- Alves, G., et al.
(författare)
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Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach
- 2022
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 33:6, s. 917-931
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Tidskriftsartikel (refereegranskat)abstract
- Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. To meet this goal from the mass spectrometry aspect, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of this augmented workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation shows that MiCId's workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in identifying antibiotic resistance proteins. In addition to having high sensitivity and precision, MiCId's workflow is fast and portable, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. It performs microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6-17 min per MS/MS sample using computing resources that are available in most desktop and laptop computers. We have also demonstrated other use of MiCId's workflow. Using MS/MS data sets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other being multidrug-resistant, we applied MiCId's workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCId's conclusions agree with the published study.
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| 7. |
- Amini, Nahid, et al.
(författare)
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SALDI-MS Signal Enhancement Using Oxidized Graphitized Carbon Black Nanoparticles
- 2009
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 20:6, s. 1207-1213
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Tidskriftsartikel (refereegranskat)abstract
- The signal intensity of low-molecular-weight compounds analyzed using surface-assisted laserdesorption/ionization time-of-flight mass spectrometry (SALDI-TOF-MS) was significantlyenhanced when oxidized graphitized carbon black (GCB) particles were used as the desorption/ionization surface. The surface of oxidized GCB contains more carboxylic acid groupsthan non-oxidized GCB. Carboxylic acid groups enhance the efficiency of the ionizationprocess and the desorption of more hydrophobic compounds. A common pharmaceuticalcompound, propranolol, was successfully extracted from Baltic Sea blue mussels and quantifiedusing oxidized GCB as the SALDI surface, whereas deuterated propranolol was used asthe internal standard. The calibration curve showed a wide linear dynamic range of response(0.1–20 g/mL) and good reproducibility (RSD 10%). It was not possible to detectpropranolol in Baltic Sea blue mussels when non-oxidized GCB was used as the SALDI surface.
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| 8. |
- Aminlashgari, Nina, et al.
(författare)
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Surface Assisted Laser Desorption Ionization-Mass Spectrometry (SALDI-MS) for Analysis of Polyester Degradation Products
- 2012
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 23:6, s. 1071-1076
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Tidskriftsartikel (refereegranskat)abstract
- Novel surface assisted laser desorption ionization-mass spectrometry (SALDI-MS) method was developed for rapid analysis of low molecular mass polyesters and their degradation products by laser desorption ionization-mass spectrometry. Three polycaprolactone materials were analyzed by the developed method before and after hydrolytic degradation. The signal-to-noise values obtained by SALDI-MS were 20-100 times higher compared with the ones obtained by using traditional MALDI-MS matrices. A clean background at low mass range and higher resolution was obtained by SALDI-MS. Different nanoparticle, cationizing agent, and solvent combinations were evaluated. Halloysite nanoclay and magnesium hydroxide showed the best potential as SALDI surfaces. The SALDI-MS spectrum of the polyester hydrolysis products was verified by ESI-MS. The developed SALDI-MS method possesses several advantages over existing methods for similar analyses.
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| 9. |
- Bazoti, Fotini N., et al.
(författare)
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Localization of the noncovalent binding site between amyloid-beta-peptide and oleuropein using electrospray ionization FT-ICR mass spectrometry.
- 2008
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 19:8, s. 1078-1085:19, s. 1078-1085
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Tidskriftsartikel (refereegranskat)abstract
- Abnormal accumulation and aggregation of amyloid-alpha-peptide (AM) eventually lead to the formation and cerebral deposition of amyloid plaques, the major pathological hallmark in Alzheimer's disease (AD). Oleuropein (OE), an Olea europaea L. derived polyphenol, exhibits a broad range of pharmacological properties, such as antioxidant, anti-inflammatory, and antiatherogenic, which could serve as combative mechanisms against several reported pathways involved in the pathophysiology of AD. The reported noncovalent interaction between AM and OE could imply a potential antiamyloidogenic role of the latter on the former via stabilization of its structure and prevention of the adaptation of a toxic beta-sheet conformation. The established P-sheet conformation of the AM hydrophobic carboxy-terminal region and the dependence of its toxicity and aggregational propensity on its secondary structure make the determination of the binding site between AM and OF highly important for assessing the role of the interaction. In this study, two different proteolytic digestion protocols, in conjunction with high-sensitivity electrospray ionization mass spectrometric analysis of the resulting peptide fragments, were used to determine the noncovalent binding site of OE on AM and revealed the critical regions for the interaction.
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| 10. |
- Bazoti, Fotini N., et al.
(författare)
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Noncovalent interaction between amyloid-b-peptide (1-40) and oleuropein studied by electrospray ionization mass spectrometry.
- 2006
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 17:4, s. 568-575
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Tidskriftsartikel (refereegranskat)abstract
- Beta amyloid peptide (A beta) is the major proteinaceous component of senile plaques formed in Alzheimer's disease (AD) brain. The aggregation of A beta is associated with neurodegeneration, loss of cognitive ability, and premature death. It has been suggested that oxidative stress and generation of free radical species have implications in the fibrillation of A beta and its subsequent neurotoxicity. For this reason, it is proposed that antioxidants may offer a protective or therapeutic alternative against amyloidosis. This study is the first report of the formation of the noncovalent complex between A beta or its oxidized form and the natural derived antioxidant oleuropein (OE) by electrospray ionization mass spectrometry (ESI MS). ESI MS allowed the real time monitoring of the complex formation between A beta, OE, and variants thereof. Several experimental conditions, such as elevated orifice potential, low pH values, presence of organic modifier, and ligand concentration were examined, to assess the specificity and the stability of the formed noncovalent complexes.
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