Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Perseus translates proteomics data

27.07.2016

Do you speak -omics? If you don't, Perseus – www.perseus-framework.org might be able to help you. Researchers from the Max Planck Institute of Biochemistry in Martinsried have developed this free software platform for users of high-throughput techniques, such as mass spectrometry, in order to translate raw biological data into relevant findings. As reported in the current issue of Nature Methods, molecular signatures from cells, tissue and body fluids can be identified and characterized on this platform without the need for bioinformatic training. Perseus was designed to deal with proteomic studies. It has also proven itself in other molecular studies and will be expanded accordingly.

Do you speak -omics? If you don't, Perseus – www.perseus-framework.org might be able to help you. Researchers in Martinsried have developed this free software platform for users of high-throughput techniques, such as mass spectrometry, in order to translate raw biological data into relevant findings.


Researchers in the life sciences can now use the free software platform www.perseus-framework.org to analyze raw data from high-throughput techniques.

Tyanova, Krause © MPI of Biochemistry

As reported in the current issue of Nature Methods, molecular signatures from cells, tissue and body fluids can be identified and characterized on this platform without the need for bioinformatic training. Perseus was designed to deal with proteomic studies in which data on thousands of proteins is processed. It has, however, also proven itself in other molecular studies and will be expanded accordingly.

Absolutely nothing in an organism works without proteins. These molecules operate as molecular machines, act as building materials and appear in a variety of other roles. However, they are rarely lone warriors, with the result that analyzing the sum total of all proteins in a cell, a tissue, a body fluid or even in an entire organism is essential.

This can establish when and where a particular molecule appears in what quantity and with whom it interacts. Corresponding approaches exist for other biological molecules as well. Modern high-throughput techniques such as mass spectrometry provide the necessary raw data, often from several thousand different proteins.

Meaningful and relevant relationships need to be extracted and interpreted from these mountains of data. Given the huge quantity of raw data, this is now possible only with the help of computer-based methods. “These steps have become a bottleneck in high-throughput studies,” says Jürgen Cox from the Max Planck Institute of Biochemistry in Martinsried, who leads the development of the Perseus platform.

“We assume that there are still a lot of potentially important findings hidden in existing proteomics data only because the appropriate computer methods are technically too complex or the data does not end up with the researchers who could grasp the biological importance of the results.”

Cox and his team have therefore ensured that individual algorithms no longer have to find their way to the right laboratories. Instead, researchers can collect their software where they need it at a central point. Among other things, the Perseus platform allows highly varying protein amounts to be screened and analyzed.

It can quantify proteins and capture their interactions and modifications. The platform incorporates statistical methods, which identify patterns, analyze time series data, test multiple hypotheses and compare data obtained from different techniques.

No previous knowledge or special training is required as the platform is an interactive environment involving user participation and featuring highly intuitive operability. The site features helpful descriptions of the functions and parameters, while YouTube videos explaining how to use the platform and a Google group with more than 1,400 active users also provide assistance. “Perseus successfully completed the first pilot tests, also in extremely complex interdisciplinary investigations,” as Cox relates. “In fact, the software not only runs on proteomic data, but also in other large data sets. In future, we will adapt the programs for metabolomic studies.”

Original publication:
S. Tyanova, T. Temu, P. Sinitcyn, A. Carlson, M.Y. Hein, T. Geiger, M. Mann & J. Cox: The Perseus computational platform for comprehensive analysis of (prote)omics data, Nature Methods, June 2016
DOI: 10.1038/nmeth.3901

Contact:
Prof. Jürgen Cox, PhD
Computational Systems Biochemistry
Max-Planck-Institut für Biochemie
Am Klopferspitz 18
82152 Martinsried
E-Mail: cox@biochem.mpg.de
www.biochem.mpg.de/cox

Dr. Christiane Menzfeld
Public Relations
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 Martinsried
Tel. +49 89 8578-2824
E-Mail: pr@biochem.mpg.de
www.biochem.mpg.de

Weitere Informationen:

http://www.biochem.mpg.de/en - homepage max planck institute of biochemistry
http://www.biochem.mpg.de/cox - homepage research group "Computational Systems Biochemistry“ (Jürgen Cox)

Dr. Christiane Menzfeld | Max-Planck-Institut für Biochemie

Further reports about: Biochemie Biochemistry Cox Max Planck Institute Max-Planck-Institut Perseus

More articles from Life Sciences:

nachricht Bacteria as pacemaker for the intestine
22.11.2017 | Christian-Albrechts-Universität zu Kiel

nachricht Researchers identify how bacterium survives in oxygen-poor environments
22.11.2017 | Columbia University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Nanoparticles help with malaria diagnosis – new rapid test in development

The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.

Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

Im Focus: Novel Nano-CT device creates high-resolution 3D-X-rays of tiny velvet worm legs

Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.

During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....

Im Focus: Researchers Develop Data Bus for Quantum Computer

The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.

Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

Corporate coworking as a driver of innovation

22.11.2017 | Business and Finance

PPPL scientists deliver new high-resolution diagnostic to national laser facility

22.11.2017 | Physics and Astronomy

Quantum optics allows us to abandon expensive lasers in spectroscopy

22.11.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>