Quantum leap in the reliability of mass spectrometry-based proteomics
Modern mass spectrometry systems enable scientists to routinely determine the quantitative composition of cells or tissue samples. However, different analysis software packages often produce different results from the same raw data. An international team of researchers led by Professor Stefan Tenzer from the Mainz University Medical Center has now addressed this problem.
In the framework of an international collaboration with leading laboratories worldwide, the team has compared and modified various analysis software packages to ensure that the different software solutions produce consistent results. A wide range of laboratories around the world are benefiting from this work, which enables researchers to analyze or compare the results of quantitative proteomics assays in a standardized way. This is crucial to detect certain organic diseases, such as cancer, at an early stage. The results of Tenzer and his team have now been published in the highly respected academic journal, Nature Biotechnology.
When doctors want to find the cause of a particular illness, they have to take samples of cells or bodily fluids. These samples are then analyzed by modern Omics techniques which enable to reproducibly quantify thousands of proteins across large numbers of samples to identify novel biomarkers for diseases. The analysis of these highly complex datasets critically depends on specialized software packages. Unfortunately, different software packages sometimes deliver divergent results from the same raw data, thus complicating the analysis.
This is exactly the problem that Professor Stefan Tenzer and his team from the Institute of Immunology at the University Medical Center of Johannes Gutenberg University Mainz (JGU) set out to resolve. "We wanted to find a way of optimally comparing samples, even when different analysis software sometimes produces deviating results," explained Tenzer. For his latest project he used two defined samples with precisely defined ratios of constituents.
The bioinformatics specialists in Tenzer's team, Dr. Pedro Navarro and Dr. Jörg Kuharev, developed a specialist piece of software, termed LFQbench. This allowed the team to study the differences between the various analysis programs in detail. "Using LFQbench, we were able to show that the results delivered by the various programs differed significantly," explained Navarro. "This finding alone has significant impact for the scientific community.
But we have taken the project a step further: Our close collaboration with the developers of the individual programs enabled them to modify and improve their analysis packages so that they now produce highly convergent results," added Tenzer. This broadens the scope of applications of the mass spectrometry technique known as quantitative proteomics. A proteome is the entirety of proteins expressed by a cell. "This means that in the future, mass spectrometry will be able to provide even more benefits both in basic research and as a potential diagnostic tool," Tenzer pointed out.
"This development represents a breakthrough for mass spectrometry-based quantitative proteomics and makes this method increasingly important as a standard procedure for use in the diagnosis of various disorders, such as cancer or allergies," emphasized the Chief Scientific Officer of the Mainz University Medical Center, Professor Ulrich Förstermann. "I am particularly proud that our researchers are delivering applied research with such significant impact."
The pioneering results were achieved under the aegis of the technology platform "Mass Spectrometry and Quantitative Proteomics" based at the Research Center for Immunotherapy (FZI) at Johannes Gutenberg University Mainz (JGU). "This success demonstrates the necessity of combining different areas of expertise in technology platforms at the University Medical Center. Without central support, it is nowadays almost impossible to accomplish achievements of this kind," said Professor Hansjörg Schild, Director of the Institute of Immunology and coordinator of the FZI for many years.
Over recent years, Professor Stefan Tenzer and his team in Mainz have developed several improvements to the techniques used for mass spectrometry-based quantitative proteomics. These methods reproducibly detect and quantify thousands of proteins in samples of cells, tissues, or bodily fluids, and enable researchers to identify proteins that are differentially expressed. "The years of work within the technology platform, especially in international joint projects, have paid off in terms of this quantum leap forward in mass spectrometry-based quantitative proteomics," concluded Tenzer.
"A multicenter study benchmarks software tools for label-free proteome quantification"
Pedro Navarro1,11, Jörg Kuharev1,11, Ludovic C Gillet2, Oliver M. Bernhardt3, Brendan MacLean4, Hannes L. Röst2, Stephen A. Tate5, Chih-Chiang Tsou6, Lukas Reiter3, Ute Distler1, George Rosenberger2,7, Yasset Perez-Riverol8, Alexey I. Nesvizhskii6,9, Ruedi Aebersold2,10, Stefan Tenzer1
1 Institute of Immunology, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
2 Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland
3 Biognosys AG, Schlieren, Switzerland
4 Department of Genome Sciences, University of Washington, Seattle, Washington, USA
5 AB Sciex, Concord, Ontario, Canada
6 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
7 PhD Program in Systems Biology, University of Zurich and Eidgenoessische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
8 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
9 Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
10 Faculty of Science, University of Zurich, Zurich, Switzerland
11 These authors contributed equally to this work.
Professor Stefan Tenzer
Head of the Core Facility for Mass Spectrometry
Institute of Immunology
Mainz University Medical Center
Oliver Kreft, Press and Public Relations, Mainz University Medical Center
phone +49 6131 17-7424, fax +49 6131 17-3496, e-mail: firstname.lastname@example.org
Petra Giegerich | idw - Informationsdienst Wissenschaft
Newly designed molecule binds nitrogen
23.02.2018 | Julius-Maximilians-Universität Würzburg
Atomic Design by Water
23.02.2018 | Max-Planck-Institut für Eisenforschung GmbH
A newly developed laser technology has enabled physicists in the Laboratory for Attosecond Physics (jointly run by LMU Munich and the Max Planck Institute of Quantum Optics) to generate attosecond bursts of high-energy photons of unprecedented intensity. This has made it possible to observe the interaction of multiple photons in a single such pulse with electrons in the inner orbital shell of an atom.
In order to observe the ultrafast electron motion in the inner shells of atoms with short light pulses, the pulses must not only be ultrashort, but very...
A group of researchers led by Andrea Cavalleri at the Max Planck Institute for Structure and Dynamics of Matter (MPSD) in Hamburg has demonstrated a new method enabling precise measurements of the interatomic forces that hold crystalline solids together. The paper Probing the Interatomic Potential of Solids by Strong-Field Nonlinear Phononics, published online in Nature, explains how a terahertz-frequency laser pulse can drive very large deformations of the crystal.
By measuring the highly unusual atomic trajectories under extreme electromagnetic transients, the MPSD group could reconstruct how rigid the atomic bonds are...
Quantum computers may one day solve algorithmic problems which even the biggest supercomputers today can’t manage. But how do you test a quantum computer to...
For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.
In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...
Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale
Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...
15.02.2018 | Event News
13.02.2018 | Event News
12.02.2018 | Event News
23.02.2018 | Physics and Astronomy
23.02.2018 | Health and Medicine
23.02.2018 | Physics and Astronomy