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| 2. |
- Billeter, Martin, 1955, et al.
(författare)
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Multi-way decomposition of projected spectra obtained in protein NMR
- 2007
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Ingår i: Proc. Appl. Math. Mech.. ; 7, s. 1110103-1110104
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Konferensbidrag (refereegranskat)abstract
- Multidimensional nuclear magnetic resonance spectroscopy is a highly versatile tool in protein research. Experimental limitations prohibit spectra with ≥ 5 dimensions. However, similar information can be obtained by recording 2-dimensional projections. A decomposition-based approach for analyzing projections is presented and applied to a protein. The resulting resonance identification is a prerequisite for further characterization of structure, dynamics and interactions of proteins.
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| 3. |
- Billeter, Martin, 1955, et al.
(författare)
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Rapid Multidimensional NMR: Decomposition Methods and their Applications
- 2009
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Ingår i: Encyclopedia of Magnetic Resonance. - Chichester, UK : John Wiley & Sons, Ltd. ; 9
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Forskningsöversikt (refereegranskat)abstract
- A signal in an N-dimensional NMR spectrum can be characterized as a direct product of N Lorentzian functions, where each function characterizes the chemical shift and linewidth of the signal along one of the dimensions. Consequently, a complete spectrum (excluding noise) may be described in a compact form by a sum of direct products, one for each signal. This representation of a spectrum can in many cases be further compressed by characterizing several (related) signals with only one direct product. The description also applies to more general data sets, such as stacks of 2-dimensional spectra recorded for relaxation or drug discovery purposes, where the function type need no longer be Lorentzian. This view of NMR spectra serves as a basis for decomposition methods that provide a number of benefits for the interpretation of NMR data such as optimal processing with low signal-to-noise. A major interest in these decomposition tools has arisen in the context of ‘rapid’ NMR, for example with random sparse sampling of the time domain or with projection spectroscopy.
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| 4. |
- Burg, Dominic, et al.
(författare)
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Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome
- 2018
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 17:6, s. 2072-2091
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of induced sputum supematant is a minimally invasive approach to study the epithelial lining fluid and, thereby, provide insight into normal lung biology and the pathobiology of lung diseases. We present here a novel proteomics approach to sputum analysis developed within the U-BIOPRED (unbiased biomarkers predictive of respiratory disease outcomes) international project. We present practical and analytical techniques to optimize the detection of robust biomarkers in proteomic studies. The normal sputum proteome was derived using data-independent HDMSE applied to 40 healthy nonsmoking participants, which provides an essential baseline from which to compare modulation of protein expression in respiratory diseases. The "core" sputum proteome (proteins detected in >= 40% of participants) was composed of 284 proteins, and the extended proteome (proteins detected in >= 3 participants) contained 1666 proteins. Quality control procedures were developed to optimize the accuracy and consistency of measurement of sputum proteins and analyze the distribution of sputum proteins in the healthy population. The analysis showed that quantitation of proteins by HDMSE is influenced by several factors, with some proteins being measured in all participants' samples and with low measurement variance between samples from the same patient. The measurement of some proteins is highly variable between repeat analyses, susceptible to sample processing effects, or difficult to accurately quantify by mass spectrometry. Other proteins show high interindividual variance. We also highlight that the sputum proteome of healthy individuals is related to sputum neutrophil levels, but not gender or allergic sensitization. We illustrate the importance of design and interpretation of disease biomarker studies considering such protein population and technical measurement variance.
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| 5. |
- Fredriksson, Jonas, 1972, et al.
(författare)
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Automated protein backbone assignment using the projection-decomposition approach
- 2012
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Ingår i: Journal of Biomolecular NMR. - 0925-2738. ; 54:1, s. 43-51
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Tidskriftsartikel (refereegranskat)abstract
- Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CHb assignments. For the 128 residue long azurin, missing assignments mostly affect Ha and Hb. Among the remaining backbone (plus Cb) nuclei 97.5 % could be assigned with 1.0 % differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5 % of the backbone and CHbresonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach.
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| 6. |
- Gu, Irene Yu-Hua, 1953, et al.
(författare)
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Parameter Estimation of Multidimensional NMR Signals based on High-Resolution Subband Analysis of 2D NMR Projections
- 2009
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Ingår i: IEEE International Conf. Acoustics, Speech and Signal Processing (ICASSP 2009). ; , s. 497-500
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Konferensbidrag (refereegranskat)abstract
- NMR spectroscopy is a powerful technique used in protein research for comprehensive functional characterizations, e.g. structure determination at atomic resolution. Due to the molecular size (typically>1000 atoms), proteinNMR spectra contain a large number of signal frequencies. Resolving these requires high-dimensional spectroscopy. However, when the number of frequency exceeds three, conventional approaches start to demand unrealistic long experiment time, and the data analysis becomes challenging. In this paper we explore a combination of novel methods: Data from 5D NMR experiments are recorded as a series of 2D projections, which are then subjected to 2D subband filters and 2D LS-ESPRIT for estimation of signal parameters. Based on the relations established between 5D NMR signals and their 2D counterparts, projection spectroscopy allows to extract highly similar information as what would be found in conventional 5D NMR experiments; however, while the latter would require months of experiment time, the recording of all necessary projections can be accomplished within 1-2 days. Preliminary results show the efficiency of the method with respect to accuracy and resolution of the parameter estimates as compared with conventional methods.
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| 7. |
- Staykova, Doroteya, et al.
(författare)
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Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach
- 2008
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Ingår i: J Biomol NMR. - : Springer Science and Business Media LLC. - 1573-5001. ; 42:2, s. 87-97
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Tidskriftsartikel (refereegranskat)abstract
- We present an approach for the assignment of protein NMR resonances that combines established and new concepts: (a) Based on published reduced dimensionality methods, two 5-dimensional experiments are proposed. (b) Multi-way decomposition (PRODECOMP) applied simultaneously to all acquired NMR spectra provides the assignment of resonance frequencies under conditions of very low signal-to-noise. (c) Each resulting component characterizes all spin ½ nuclei in a (doubly-labeled) CβHn–CαH–C′–NH–CαH–CβHn fragment in an unambiguous manner, such that sequentially neighboring components have about four atoms in common. (d) A new routine (SHABBA) determines correlations for all component pairs based on the common nuclei; high correlation values yield sequential chains of a dozen or more components. (e) The potentially error-prone peak picking is delayed to the last step, where it helps to place the component chains within the protein sequence, and thus to achieve the final backbone assignment. The approach was validated by achieving complete backbone resonance assignments for ubiquitin. Electronic supplementary material The online version of this article (doi:10.1007/s10858-008-9265-z) contains supplementary material, which is available to authorized users.
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