| 1. |
- Branca, Rui M. M., et al.
(författare)
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HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics
- 2014
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:1, s. 59-
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Tidskriftsartikel (refereegranskat)abstract
- We present a liquid chromatography-mass spectrometry (LC-MSMS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.
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| 2. |
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| 3. |
- Wright, J. C., et al.
(författare)
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Enhanced peptide identification by electron transfer dissociation using an improved mascot percolator
- 2012
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 11:8, s. 478-491
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Tidskriftsartikel (refereegranskat)abstract
- Peptide identification using tandem mass spectrometry is a core technology in proteomics. Latest generations of mass spectrometry instruments enable the use of electron transfer dissociation (ETD) to complement collision induced dissociation (CID) for peptide fragmentation. However, a critical limitation to the use of ETD has been optimal database search software. Percolator is a postsearch algorithm, which uses semi-supervised machine learning to improve the rate of peptide spectrum identifications (PSMs) together with providing reliable significance measures. We have previously interfaced the Mascot search engine with Percolator and demonstrated sensitivity and specificity benefits with CID data. Here, we report recent developments in the Mascot Percolator V2.0 software including an improved feature calculator and support for a wider range of ion series. The updated software is applied to the analysis of several CID and ETD fragmented peptide data sets. This version of Mascot Percolator increases the number of CID PSMs by up to 80% and ETD PSMs by up to 60% at a 0.01 q-value (1% false discovery rate) threshold over a standard Mascot search, notably recovering PSMs from high charge state precursor ions. The greatly increased number of PSMs and peptide coverage afforded by Mascot Percolator has enabled a fuller assessment of CID/ETD complementarity to be performed. Using a data set of CID and ETcaD spectral pairs, we find that at a 1% false discovery rate, the overlap in peptide identifications by CID and ETD is 83%, which is significantly higher than that obtained using either stand-alone Mascot (69%) or OMSSA (39%). We conclude that Mascot Percolator is a highly sensitive and accurate post-search algorithm for peptide identification and allows direct comparison of peptide identifications using multiple alternative fragmentation techniques.
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| 4. |
- Gustafsson, Håkan, et al.
(författare)
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Magnetic and Electron Spin Relaxation Properties of (GdxY1-x)(2)O-3 (0 <= x <= 1) Nanoparticles Synthesized by the Combustion Method. Increased Electron Spin Relaxation Times with Increasing Yttrium Content
- 2011
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 115:13, s. 5469-5477
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Tidskriftsartikel (refereegranskat)abstract
- The performance of a magnetic resonance imaging contrast agent (CA) depends on several factors, including the relaxation times of the unpaired electrons in the CA. The electron spin relaxation time may be a key factor for the performance of new CAs, such as nanosized Gd2O3 particles. The aim of this work is, therefore, to study changes in the magnetic susceptibility and the electron spin relaxation time of paramagnetic Gd2O3 nanoparticles diluted with increasing amounts of diamagnetic Y2O3. Nanoparticles of (GdxY1-x)(2)O-3 (0 <= x <= 1) were prepared by the combustion method and thoroughly characterized (by X-ray diffraction, transmission electron microscopy, thermogravimetry coupled with mass spectroscopy, photoelectron spectroscopy, Fourier transform infrared spectroscopy, and magnetic susceptibility measurements). Changes in the electron spin relaxation time were estimated by observations of the signal line width in electron paramagnetic resonance spectroscopy, and it was found that the line width was dependent on the concentration of yttrium, indicating that diamagnetic Y2O3 may increase the electron spin relaxation time of Gd2O3 nanoparticles.
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| 5. |
- Gustafsson, Håkan, 1976-, et al.
(författare)
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Magnetic and Electron Spin Relaxation Properties of (GdxY1-x)2O3 (0 ≤ x ≤ 1) Nanoparticles Synthesized by the Combustion Method. Increased Electron Spin Relaxation Times with Increasing Yttrium Content
- 2011
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Ingår i: The Journal of Physical Chemistry C. - United States : American Chemical Society. - 1932-7447 .- 1932-7455. ; 115:13, s. 5469-5477
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Tidskriftsartikel (refereegranskat)abstract
- The performance of a magnetic resonance imaging contrast agent (CA) depends on several factors, including the relaxation times of the unpaired electrons in the CA. The electron spin relaxation time may be a key factor for the performance of new CAs, such as nanosized Gd2O3 particles. The aim of this work is, therefore, to study changes in the magnetic susceptibility and the electron spin relaxation time of paramagnetic Gd2O3 nanoparticles diluted with increasing amounts of diamagnetic Y2O3. Nanoparticles of (GdxY1-x)2O3 (0 e x e 1) were prepared by the combustion method and thoroughly characterized (by X-ray di.raction, transmission electron microscopy, thermogravimetry coupled with mass spectroscopy, photoelectron spectroscopy, Fourier transform infrared spectroscopy, and magnetic susceptibility measurements). Changes in the electron spin relaxation time were estimated by observations of the signal line width in electron paramagnetic resonance spectroscopy, and it was found that the line width was dependent on the concentration of yttrium, indicating that diamagnetic Y2O3 may increase the electron spin relaxation time of Gd2O3 nanoparticles.
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| 6. |
- Lehmuskero, Anni, 1982, et al.
(författare)
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Plasmonic particles set into fast orbital motion by an optical vortex beam WARI SC, 1992, JOURNAL OF MODERN OPTICS, V39, P1097
- 2014
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Ingår i: Optics Express. - : The Optical Society. - 1094-4087 .- 1094-4087. ; 22:4, s. 4349-4356
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Tidskriftsartikel (refereegranskat)abstract
- We optically trap plasmonic gold particles in two dimensions and set them into circular motion around the optical axis using a helically phased vortex laser beam. The orbiting frequency of the particles reaches 86 Hz, which corresponds to a particle velocity of the order 1 mm per second, for an incident laser power of a few tens of milliwatts. The experimentally determined orbiting frequencies are found to be well in line with the notion that the beam carries an orbital angular momentum of hl per photon. (C) 2014 Optical Society of America
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| 7. |
- Moruz, Luminita, et al.
(författare)
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Chromatographic retention time prediction for posttranslationally modified peptides
- 2012
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 12:8, s. 1151-1159
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Tidskriftsartikel (refereegranskat)abstract
- Retention time prediction of peptides in liquid chromatography has proven to be a valuable tool for mass spectrometry-based proteomics, especially in designing more efficient procedures for state-of-the-art targeted workflows. Additionally, accurate retention time predictions can also be used to increase confidence in identifications in shotgun experiments. Despite these obvious benefits, the use of such methods has so far not been extended to (posttranslationally) modified peptides due to the absence of efficient predictors for such peptides. We here therefore describe a new retention time predictor for modified peptides, built on the foundations of our existing Elude algorithm. We evaluated our software by applying it on five types of commonly encountered modifications. Our results show that Elude now yields equally good prediction performances for modified and unmodified peptides, with correlation coefficients between predicted and observed retention times ranging from 0.93 to 0.98 for all the investigated datasets. Furthermore, we show that our predictor handles peptides carrying multiple modifications as well. This latest version of Elude is fully portable to new chromatographic conditions and can readily be applied to other types of posttranslational modifications. Elude is available under the permissive Apache2 open source License at or can be run via a web-interface at.
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