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- Hakansson, K, et al.
(författare)
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Mechanistic studies of multipole storage assisted dissociation
- 2000
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Ingår i: JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY. - : ELSEVIER SCIENCE INC. - 1044-0305. ; 11:3, s. 210-217
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Tidskriftsartikel (refereegranskat)abstract
- The degree and onset of fragmentation in multipole storage assisted dissociation (MSAD) have been investigated as functions of several hexapole parameters. Strict studies of hexapole charge density (number of ions injected) and hexapole storage time were
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- Johansson, J, et al.
(författare)
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Pulmonary surfactant: emerging protein analogues
- 1999
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Ingår i: BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy. - : Springer Science and Business Media LLC. - 1173-8804. ; 11:2, s. 71-77
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Johansson, J, et al.
(författare)
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Synthetic surfactant protein analogues
- 1998
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Ingår i: Biology of the neonate. - : S. Karger AG. - 0006-3126. ; 7474 Suppl 1, s. 9-14
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Tidskriftsartikel (refereegranskat)abstract
- Surfactant preparations for the treatment of respiratory distress syndrome (RDS) that contain phospholipids and small amounts of the two hydrophobic proteins, SP-B and SP-C, are presently obtained from animal lungs. Since structural information about SP-B and SP-C is available, it appears possible to design analogues that can replace the native proteins in synthetic surfactants. SP-C contains a single helix, but analogues with the poly-Val sequence of the native molecule do not fold into a native-like α-helical conformation. However, replacement of all Val with Leu yields efficient folding into a helical structure and Leu-based SP-C analogues effectively accelerate spreading of surfactant lipids and exhibit some physiological activity in animal models of RDS. The inferior in vivo activity of synthetic surfactants containing SP-C only compared to that of surfactant preparations derived from natural sources may be caused by a lack of covalently linked palmitoyl groups in the analogues and/or absence of SP-B. SP-B is significantly larger than SP-C and has a tertiary fold of several amphipathic helices in a dimeric structure. A single simplified amphipathic helical peptide containing only Leu and Lys does not mimic the surface properties of SP-B in vitro. These circumstances make the design of SP-B analogues from solely structural considerations less likely to be successful than in the case of SP-C.
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- Johansson, O., et al.
(författare)
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Electron donor-acceptor dyads based on ruthenium(II) bipyridine and terpyridine complexes bound to naphthalenediimide
- 2003
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 42:9, s. 2908-2918
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Tidskriftsartikel (refereegranskat)abstract
- Two series of photosensitizer-electron acceptor complexes have been synthesized and fully characterized: ruthenium(11) tris(bipyridine) {[Ru-II(bpy)(2)(bpy-X-NDI)], where X = -CH2-, tolylene, or phenylene, bpy is 2,2'-bipyridine, and NDI is naphthalenediimide} and ruthenium(II) bis(terpyridine) {[Ru-II(Y-tpy)(tpy-X-NDI)], where Y = H or tolyl and X = tolylene or phenylene, and tpy = 2,2':6',2-terpyridine}. The complexes have been studied by cyclic and differential pulse voltammetry and by steady state and time-resolved absorption and emission techniques. Rates for forward and backward electron transfer have been investigated, following photoexcitation of the ruthenium(II) polypyridine moiety. The terpyridine complexes were only marginally affected by the linked diimide unit, and no electron transfer was observed. In the bipyridine complexes we achieved efficient charge separation. For the complexes containing a phenyl link between the ruthenium(II) and diimide moieties, our results suggest a biphasic forward electron-transfer reaction, in which 20% of the charge-separated state was formed via population of the naphthalenediimide triplet state.
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- Lee, J. -Y, et al.
(författare)
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ABRF Proteome Informatics Research Group (iPRG) 2016 Study : Inferring Proteoforms from Bottom-up Proteomics Data
- 2018
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Ingår i: Journal of biomolecular techniques : JBT. - : NLM (Medline). - 1943-4731 .- 1524-0215. ; 29:2, s. 39-45
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Tidskriftsartikel (refereegranskat)abstract
- This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of 4 Escherichia coli samples spiked with different equimolar mixtures of small recombinant proteins selected to mimic pairs of homologous proteins. Participants were given raw data and a sequence file and asked to identify the proteins and provide estimates on the FDR at the proteoform level. As part of this study, we tested a new submission system with a format validator running on a virtual private server (VPS) and allowed methods to be provided as executable R Markdown or IPython Notebooks. The task was perceived as difficult, and only eight unique submissions were received, although those who participated did well with no one method performing best on all samples. However, none of the submissions included a complete Markdown or Notebook, even though examples were provided. Future iPRG studies need to be more successful in promoting and encouraging participation. The VPS and submission validator easily scale to much larger numbers of participants in these types of studies. The unique "ground-truth" dataset for proteoform identification generated for this study is now available to the research community, as are the server-side scripts for validating and managing submissions.
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- Ohana, D., et al.
(författare)
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Identification of meat products by shotgun spectral matching
- 2016
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 203, s. 28-34
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Tidskriftsartikel (refereegranskat)abstract
- A new method, based on shotgun spectral matching of peptide tandem mass spectra, was successfully applied to the identification of different food species. The method was demonstrated to work on raw as well as processed samples from 16 mammalian and 10 bird species by counting spectral matches to spectral libraries in a reference database with one spectral library per species. A phylogenetic tree could also be constructed directly from the spectra. Nearly all samples could be correctly identified at the species level, and 100% at the genus level. The method does not use any genomic information and unlike targeted methods, no prior knowledge of genetic variation within a genus or species is necessary.
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