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 A novel synthetic antibody enables conditional “protein knockdown” in vertebrates
20.08.2018 | Technische Universität Dresden

nachricht Climate Impact Research in Hannover: Small Plants against Large Waves
17.08.2018 | Leibniz Universität Hannover

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: It’s All in the Mix: Jülich Researchers are Developing Fast-Charging Solid-State Batteries

There are currently great hopes for solid-state batteries. They contain no liquid parts that could leak or catch fire. For this reason, they do not require cooling and are considered to be much safer, more reliable, and longer lasting than traditional lithium-ion batteries. Jülich scientists have now introduced a new concept that allows currents up to ten times greater during charging and discharging than previously described in the literature. The improvement was achieved by a “clever” choice of materials with a focus on consistently good compatibility. All components were made from phosphate compounds, which are well matched both chemically and mechanically.

The low current is considered one of the biggest hurdles in the development of solid-state batteries. It is the reason why the batteries take a relatively long...

Im Focus: Color effects from transparent 3D-printed nanostructures

New design tool automatically creates nanostructure 3D-print templates for user-given colors
Scientists present work at prestigious SIGGRAPH conference

Most of the objects we see are colored by pigments, but using pigments has disadvantages: such colors can fade, industrial pigments are often toxic, and...

Im Focus: Unraveling the nature of 'whistlers' from space in the lab

A new study sheds light on how ultralow frequency radio waves and plasmas interact

Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

LaserForum 2018 deals with 3D production of components

17.08.2018 | Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

 
Latest News

Quantum bugs, meet your new swatter

20.08.2018 | Information Technology

A novel synthetic antibody enables conditional “protein knockdown” in vertebrates

20.08.2018 | Life Sciences

Metamolds: Molding a mold

20.08.2018 | Information Technology

VideoLinks
Science & Research
Overview of more VideoLinks >>>