Benchmarking Mass Spectrometry-Based Proteomics

October 26, 2016
Benchmarking Mass Spectrometry-Based Proteomics
Source: Stefan Tenzer, Mainz University Medical Center

An international team of researchers led scientists at Mainz University Medical Center in Germany has addressed the issue of different analysis software packages for mass spectrometry producing different results from the same raw data. The new study—published recently in Nature Biotechnology under an article entitled “A multicenter study benchmarks software tools for label-free proteome quantification”—compared and modified various analysis software packages to ensure that the different software solutions produce consistent results.

"We wanted to find a way of optimally comparing samples, even when different analysis software sometimes produces deviating results," explained senior study investigator Stefan Tenzer, Ph.D., group leader at the Mainz Institute for Immunology. 

The scientists devised a solution that first utilized two samples with precisely defined ratios of constituents. Next bioinformatics specialists within the research team 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," noted lead study investigator Pedro Navarro, Ph.D., who was, until recently, a postdoctoral researcher at the University of Mainz.

"This finding alone has significant impact on 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 Dr. Tenzer.

Modern mass spectrometry systems enable scientists to routinely determine the quantitative composition of cells or tissue samples. Furthermore, 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 various diseases, such as cancer, at an early stage.

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 scores 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.

The findings from this new study broaden 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," Dr. Tenzer stated.

"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," remarked Ulrich Förstermann, Ph.D., professor and chief scientific officer of the Mainz University Medical Center, who was not directly involved with the study. "I am particularly proud that our researchers are delivering applied research with such significant impact."

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