Ruedi Aebersold

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Ruedi Aebersold
Ruedi Aebersold 2012.JPG
Ruedi Aebersold
BornSeptember 12, 1954 [1]
Switzerland
Alma mater University of Basel
Scientific career
Fields Proteomics
Institutions ETH Zurich, Institute for Systems Biology
Thesis Structure-function relationships of hybridoma-derived monoclonal antibodies against streptococcal A group polysaccharide. (1983)
Doctoral advisor Dietmar G. Braun
Other academic advisors Leroy Hood

Rudolf Aebersold (better known as Ruedi Aebersold; born September 12, 1954 [1] ) is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. [2] He was one of the founders of the Institute for Systems Biology in Seattle, Washington, United States where he previously had a research group. [3]

Aebersold is known for the development and application of targeted proteomics techniques in the field of biomedical research, in order to understand the function, interaction and localization of each protein in the cell and its changes in disease states. [4] [5] [6] To this end, Ruedi Abersold has made significant contributions in the development and application of targeted proteomics methods, including selected reaction monitoring [7] [8] [9] and data-independent acquisition. [10] [11] Ruedi Aebersold is also recognized for its contributions in the development of standard formats and open source software for the analysis and storage of mass spectrometry and proteomics data, [12] and he is one of the inventors of the Isotope-Coded Affinity Tag (ICAT) technique for quantitative proteomics, a technique that measures the relative quantities of proteins between two sample by using tags containing stable isotopes of different masses. [13] [14]

Aebersold is co-founder and scientific advisor of the companies ProteoMediX [15] and Biognosys. [16]

Honors and awards

Related Research Articles

<span class="mw-page-title-main">Proteome</span> Set of proteins that can be expressed by a genome, cell, tissue, or organism

The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.

<span class="mw-page-title-main">Proteomics</span> Large-scale study of proteins

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.

Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins (proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here.

<span class="mw-page-title-main">Stable isotope labeling by amino acids in cell culture</span>

Stable isotope labeling by/with amino acids in cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitative proteomics.

The Association of Biomolecular Resource Facilities (ABRF) is dedicated to advancing core and research biotechnology laboratories through research, communication, and education. ABRF members include over 2000 scientists representing 340 different core laboratories in 41 countries, including those in industry, government, academic and research institutions.

The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra.

PEAKS is a proteomics software program for tandem mass spectrometry designed for peptide sequencing, protein identification and quantification.

<span class="mw-page-title-main">Quantitative proteomics</span> Analytical chemistry technique

Quantitative proteomics is an analytical chemistry technique for determining the amount of proteins in a sample. The methods for protein identification are identical to those used in general proteomics, but include quantification as an additional dimension. Rather than just providing lists of proteins identified in a certain sample, quantitative proteomics yields information about the physiological differences between two biological samples. For example, this approach can be used to compare samples from healthy and diseased patients. Quantitative proteomics is mainly performed by two-dimensional gel electrophoresis (2-DE), preparative native PAGE, or mass spectrometry (MS). However, a recent developed method of quantitative dot blot (QDB) analysis is able to measure both the absolute and relative quantity of an individual proteins in the sample in high throughput format, thus open a new direction for proteomic research. In contrast to 2-DE, which requires MS for the downstream protein identification, MS technology can identify and quantify the changes.

<span class="mw-page-title-main">ABLIM1</span> Protein-coding gene in the species Homo sapiens

Actin binding LIM protein 1, also known as ABLIM1, is a protein which in humans is encoded by the ABLIM1 gene.

An isotope-coded affinity tag (ICAT) is an in-vitro isotopic labeling method used for quantitative proteomics by mass spectrometry that uses chemical labeling reagents. These chemical probes consist of three elements: a reactive group for labeling an amino acid side chain, an isotopically coded linker, and a tag for the affinity isolation of labeled proteins/peptides. The samples are combined and then separated through chromatography, then sent through a mass spectrometer to determine the mass-to-charge ratio between the proteins. Only cysteine containing peptides can be analysed. Since only cysteine containing peptides are analysed, often the post translational modification is lost.

The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification.

OpenMS is an open-source project for data analysis and processing in mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, MacOS and Linux.

<span class="mw-page-title-main">Selected reaction monitoring</span> Tandem mass spectrometry method

Selected reaction monitoring (SRM), also called multiple reaction monitoring (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product of a fragmentation reaction of the precursor ions is selected in the second mass spectrometer stage for detection.

The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.

<span class="mw-page-title-main">Albert J. R. Heck</span> Dutch chemist

Albert J.R. Heck is a Dutch scientist and professor at Utrecht University, the Netherlands in the field of mass spectrometry and proteomics. He is known for his work on technologies to study proteins in their natural environment, with the aim to understand their biological function. Albert Heck was awarded the Spinoza Prize in 2017, the highest scientific award in the Netherlands.

In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected m/z range are fragmented and analyzed in a second stage of tandem mass spectrometry. Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time or by sequentially isolating and fragmenting ranges of m/z. DIA is an alternative to data-dependent acquisition (DDA) where a fixed number of precursor ions are selected and analyzed by tandem mass spectrometry.

Anne-Claude Gingras is a senior investigator at Lunenfeld-Tanenbaum Research Institute, and a professor in the department of molecular genetics at the University of Toronto. She is an expert in mass spectrometry based proteomics technology that allows identification and quantification of protein from various biological samples.

<span class="mw-page-title-main">Paola Picotti</span> Italian biologist and academic

Paola Picotti is an Italian biologist who is Professor for Molecular Systems Biology at ETH Zürich. She is Deputy Head of the Institute for Molecular Systems Biology. Her research investigates how the conformational changes of proteins impact cellular networks. She was awarded the 2020 ETH Zürich Rössler Prize and the 2019 EMBO Gold Medal.

<span class="mw-page-title-main">Markus Ralser</span> Italian biologist

Markus Ralser is an Italian biologist. His main research interest is metabolism of microorganisms. He is also known for his work on the origin of metabolism during the origin of life, and proteomics.

References

  1. 1 2 3 4 5 "Curriculum Vitae – Ruedi Aebersold" (PDF). Retrieved 2 December 2012.
  2. ↑ "ETH – IMSB Prof. Ruedi Aebersold" . Retrieved 2011-07-26.
  3. ↑ "Institute for Systems Biology: Aebersold Group". Archived from the original on 2011-07-20. Retrieved 2011-07-26.
  4. ↑ Aebersold R, Mann M (March 2003). "Mass spectrometry-based proteomics". Nature. 422 (6928): 198–207. Bibcode:2003Natur.422..198A. doi:10.1038/nature01511. PMID   12634793. S2CID   118260.
  5. ↑ Aebersold R, Mann M (September 2016). "Mass-spectrometric exploration of proteome structure and function". Nature. 537 (7620): 347–55. Bibcode:2016Natur.537..347A. doi:10.1038/nature19949. PMID   27629641. S2CID   4448087.
  6. ↑ Bensimon A, Heck AJ, Aebersold R (2012). "Mass spectrometry-based proteomics and network biology". Annual Review of Biochemistry. 81: 379–405. doi:10.1146/annurev-biochem-072909-100424. PMID   22439968.
  7. ↑ Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R (August 2009). "Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics". Cell. 138 (4): 795–806. doi:10.1016/j.cell.2009.05.051. PMC   2825542 . PMID   19664813.
  8. ↑ Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R (January 2010). "High-throughput generation of selected reaction-monitoring assays for proteins and proteomes". Nature Methods. 7 (1): 43–6. doi:10.1038/nmeth.1408. PMID   19966807. S2CID   193432.
  9. ↑ Picotti P, Bodenmiller B, Aebersold R (January 2013). "Proteomics meets the scientific method". Nature Methods. 10 (1): 24–7. doi:10.1038/nmeth.2291. PMID   23269373. S2CID   1362416.
  10. ↑ Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R (June 2012). "Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis". Molecular & Cellular Proteomics. 11 (6): O111.016717. doi: 10.1074/mcp.O111.016717 . PMC   3433915 . PMID   22261725.
  11. ↑ Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R (March 2015). "Building high-quality assay libraries for targeted analysis of SWATH MS data". Nature Protocols. 10 (3): 426–41. doi:10.1038/nprot.2015.015. PMID   25675208. S2CID   21543665.
  12. ↑ Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (November 2004). "A common open representation of mass spectrometry data and its application to proteomics research". Nature Biotechnology. 22 (11): 1459–66. doi:10.1038/nbt1031. PMID   15529173. S2CID   25734712.
  13. ↑ Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, Fausto N, Katze MG, Aebersold R (October 2004). "A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry". Molecular & Cellular Proteomics. 3 (10): 1039–41. doi: 10.1074/mcp.D400001-MCP200 . PMID   15269248.
  14. ↑ Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (October 1999). "Quantitative analysis of complex protein mixtures using isotope-coded affinity tags". Nature Biotechnology. 17 (10): 994–9. doi:10.1038/13690. PMID   10504701. S2CID   16273431.
  15. ↑ "ProteoMediX AG - Advisors - Zürich, Switzerland" . Retrieved 2 December 2012.
  16. ↑ "Our Team | Biognosys AG" . Retrieved 2 December 2012.
  17. 1 2 "A major honour" . Retrieved 26 December 2017.
  18. ↑ "Pionier der Eiweissforschung geehrt". 30 April 2010. Retrieved 2 December 2012.
  19. ↑ "The 2014 Thomson Medal Award IMSC 2014" . Retrieved 8 April 2014.
  20. ↑ "Ruedi Aebersold". German Academy of Sciences Leopoldina. Retrieved 26 May 2021.
  21. ↑ "Powerlist – The Analytical Scientist" . Retrieved 4 November 2015.
  22. ↑ "Bijvoet Medal". Bijvoet Center for Biomolecular Research. Retrieved 2018-04-24.
  23. ↑ Marcel Benoist Prize 2020
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