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Andreas Bamberger

Bio: Andreas Bamberger is an academic researcher from University of Freiburg. The author has contributed to research in topics: Jet (fluid) & Mass spectrometry. The author has an hindex of 7, co-authored 14 publications receiving 154 citations.

Papers
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Journal ArticleDOI
TL;DR: CoPIT was used successfully to identify the interactome of the cystic fibrosis transmembrane conductance regulator (CFTR), demonstrating its validity and performance and evidence that it can be successfully used as a general Co-IP method.
Abstract: Affinity purification coupled to mass spectrometry (AP-MS) is the method of choice for analyzing protein-protein interactions, but common protocols frequently recover only the most stable interactions and tend to result in low bait yield for membrane proteins. Here, we present a novel, deep interactome sequencing approach called CoPIT (co-interacting protein identification technology), which allows comprehensive identification and analysis of membrane protein interactomes and their dynamics. CoPIT integrates experimental and computational methods for a coimmunoprecipitation (Co-IP)-based workflow from sample preparation for mass spectrometric analysis to visualization of protein-protein interaction networks. The approach particularly improves the results for membrane protein interactomes, which have proven to be difficult to identify and analyze. CoPIT was used successfully to identify the interactome of the cystic fibrosis transmembrane conductance regulator (CFTR), demonstrating its validity and performance. The experimental step in this case achieved up to 100-fold-higher bait yield than previous methods by optimizing lysis, elution, sample clean-up and detection of interacting proteins by multidimensional protein identification technology (MudPIT). Here, we further provide evidence that CoPIT is applicable to other types of proteins as well, and that it can be successfully used as a general Co-IP method. The protocol describes all steps, ranging from considerations for experimental design, Co-IP, preparation of the sample for mass spectrometric analysis, and data analysis steps, to the final visualization of interaction networks. Although the experimental part can be performed in <3 d, data analysis may take up to a few weeks.

50 citations

Journal ArticleDOI
TL;DR: In this article, a triple-GEM detector was used to detect the ionization from 55 Fe X-rays and electrons from 106 Ru using only digital readout and two discriminator thresholds.
Abstract: We have operated a Medipix2 CMOS readout chip, with amplifying, shaping and charge discriminating front-end electronics integrated on the pixel level, as a highly segmented direct charge collecting anode in a Three-Stage Gas Electron Multiplier (Triple-GEM) to detect the ionization from 55 Fe X-rays and electrons from 106 Ru. The device allows to perform moderate energy spectroscopy measurements (20% FWHM at 5.9 keV X -rays) using only digital readout and two discriminator thresholds. Being a truly 2D detector, it allows to observe individual clusters of minimum ionizing charged particles in Ar / CO 2 (70:30) and He / CO 2 (70:30) mixtures and to achieve excellent spatial resolution for position reconstruction of primary clusters down to ∼ 50 μ m , based on the binary centroid determination method.

29 citations

Journal ArticleDOI
TL;DR: An imaging mass spectrometer that exploits the true imaging capabilities by ion optical means for the time of flight mass separation and proves high hit-multiplicity, straightforward image reconstruction, and potential for high-speed readout at 4 kHz or more.

20 citations

Journal ArticleDOI
TL;DR: In this paper, a prototype of a TPC readout with a highly pixelated CMOS ASIC, which is an option for charged particles tracking of the ILC, was investigated with a triple GEM stack with a TimePix and MediPix2 chip.
Abstract: This contribution investigates a prototype of a TPC readout with a highly pixelated CMOS ASIC, which is an option for charged particles tracking of the ILC. A triple GEM stack is joined with a TimePix and MediPix2 chip (pixel size of 55 × 55 μ m 2 ) and its readout properties are investigated with 5 GeV electrons. The spatial resolution of reconstructed cluster centers is determined as a function of the drift distance for different gases and stack configurations. Also the drift velocities are extracted. A single point resolution down to ≈ 25 μ m is achieved for small drift distances.

19 citations

Patent
16 Apr 2009
TL;DR: In this article, a method of imaging mass spectroscopy and a corresponding apparatus are provided, wherein the m/z-ratio of ions as well as the location of said ions on a sample surface are detected simultaneously in a time of flight mass spectrometer.
Abstract: A method of imaging mass spectroscopy and a corresponding apparatus are provided, wherein the m/z-ratio of ions as well as the location of said ions on a sample surface are detected simultaneously in a time of flight mass spectrometer. The detector is a semiconductor array detector comprising pixels, that each can be arranged to measure a signal intensity of a signal induced by the ions or their time of arrival. A four-dimensional image consisting of the two lateral dimensions on the sample surface, the m/z-ratio representing the ion type and the abundance of an ion type on the surface can be reconstructed from repeated measurements for which a correspondingly adapted computer program product can be involved.

19 citations


Cited by
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Journal ArticleDOI
TL;DR: Several transcribed sequences and conserved segments were identified in this cloned region and one corresponds to the cystic fibrosis gene and spans approximately 250,000 base pairs of genomic DNA.
Abstract: An understanding of the basic defect in the inherited disorder cystic fibrosis requires cloning of the cystic fibrosis gene and definition of its protein product. In the absence of direct functional information, chromosomal map position is a guide for locating the gene. Chromosome walking and jumping and complementary DNA hybridization were used to isolate DNA sequences, encompassing more than 500,000 base pairs, from the cystic fibrosis region on the long arm of human chromosome 7. Several transcribed sequences and conserved segments were identified in this cloned region. One of these corresponds to the cystic fibrosis gene and spans approximately 250,000 base pairs of genomic DNA.

803 citations

PatentDOI
TL;DR: In this paper, a process and apparatus which combine infrared laser ablation (LA) with electrospray ionization (ESI) is described, which is called atmospheric pressure mass spectrometry (APMS).
Abstract: The field of the invention is atmospheric pressure mass spectrometry (MS), and more specifically a process and apparatus which combine infrared laser ablation (LA) with electrospray ionization (ESI).

688 citations

Book
24 Mar 2005
TL;DR: This book is accompanied by a full distribution of ALBERTA (Version 1.2) on a CD including an implementation of several model problems including the direct integration of such new or improved methods in existing simulation software.
Abstract: During the last years, scientific computing has become an important research branch located between applied mathematics and applied sciences and engineering. Highly efficient numerical methods are based on adaptive methods, higher order discretizations, fast linear and non-linear iterative solvers, multi-level algorithms, etc. Such methods are integrated in the adaptive finite element software ALBERTA. It is a toolbox for the fast and flexible implementation of efficient software for real life applications, based on modern algorithms. ALBERTA also serves as an environment for improving existent, or developing new numerical methods in an interplay with mathematical analysis and it allows the direct integration of such new or improved methods in existing simulation software. The book is accompanied by a full distribution of ALBERTA (Version 1.2) on a CD including an implementation of several model problems. System requirements for ALBERTA are a Unix/Linux environment with C and FORTRAN Compilers, OpenGL graphics and GNU make. These model implementations serve as a basis for students and researchers for the implementation of their own research projects within ALBERTA.

331 citations

01 Jan 1998

244 citations

Journal ArticleDOI
24 Dec 2015-Nature
TL;DR: It is demonstrated that global remodelling of ∆F508 CFTR interactions is crucial for rescue, and comprehensive insight is provided into the molecular disease mechanisms of cystic fibrosis caused by deletion of F508.
Abstract: Deletion of phenylalanine 508 of the cystic fibrosis transmembrane conductance regulator (∆F508 CFTR) is the major cause of cystic fibrosis, one of the most common inherited childhood diseases. The mutated CFTR anion channel is not fully glycosylated and shows minimal activity in bronchial epithelial cells of patients with cystic fibrosis. Low temperature or inhibition of histone deacetylases can partly rescue ∆F508 CFTR cellular processing defects and function. A favourable change of ∆F508 CFTR protein-protein interactions was proposed as a mechanism of rescue; however, CFTR interactome dynamics during temperature shift and inhibition of histone deacetylases are unknown. Here we report the first comprehensive analysis of the CFTR and ∆F508 CFTR interactome and its dynamics during temperature shift and inhibition of histone deacetylases. By using a novel deep proteomic analysis method, we identify 638 individual high-confidence CFTR interactors and discover a ∆F508 deletion-specific interactome, which is extensively remodelled upon rescue. Detailed analysis of the interactome remodelling identifies key novel interactors, whose loss promote ∆F508 CFTR channel function in primary cystic fibrosis epithelia or which are critical for CFTR biogenesis. Our results demonstrate that global remodelling of ∆F508 CFTR interactions is crucial for rescue, and provide comprehensive insight into the molecular disease mechanisms of cystic fibrosis caused by deletion of F508.

206 citations