One of the key challenges of proteomics, the study of all proteins expressed by a cell or organism, is managing to distinguish between molecules that are structurally different yet have the same mass. This is hard because a mass spectrometer, the main apparatus used in this type of study, works like a weighing scale, sorting the molecules analysed according to their mass.
One way to reduce confusion when using a mass spectrometer is to start by submitting the sample to liquid chromatography, which separates hydrophilic (“water-loving”) proteins from hydrophobic ones.
The hydrophilic proteins enter the spectrometer first, and the most hydrophobic are left for the last, decreasing the likelihood that two different molecules with equivalent masses will be interpreted as only one by the apparatus.
“It’s like solving a jigsaw puzzle with millions of pieces. When you first open the bag, the pieces are all jumbled and overlapping. You must begin by sorting them out. As we work with proteomics, we constantly endeavor to develop more refined sorting techniques,” said Daniel Martins-de-Souza, who heads the Neuroproteomics Laboratory at the University of Campinas (UNICAMP) in Brazil.
In a study with results recently published in Proteomics and featured on the cover of the journal, Martins-de-Souza’s group optimised a method to increase the resolution of proteomic analysis by mass spectrometry.
Thanks to a combination of two other techniques – two-dimensional liquid chromatography and ion mobility – the group succeeded in identifying 10,390 proteins expressed in oligodendrocytes, the central nervous system cells responsible for producing myelin, a lipidic substance that plays an essential role in the information exchange between neurons.
In a previous study using single-dimensional liquid chromatography for pre-sorting, the group had identified only 2,290 proteins in oligodendrocytes.
“We now have a far more complete oligodendrocyte protein database, which will be useful for our own studies and those of other researchers in the field,” Martins-de-Souza said. “It’s available online, and the data can be downloaded. In addition, the optimisation technique can be used to study the proteome of any biological sample.”
With FAPESP’s support, the UNICAMP group have studied the human oligodendrocyte proteome for several years, with the aim of better understanding the causes of schizophrenia as a basis for proposing novel therapeutic approaches.
According to Martins-de-Souza, currently available treatments focus on neurons, but the neural communication failures observed in patients with schizophrenia may be due to oligodendrocyte dysfunction.
“One of our research lines consists of evaluating how the drugs used to control schizophrenia modify the oligodendrocyte proteome,” he said. “With this new methodology, we can obtain five times more information on the role of these drugs.”
The study was conducted during the postdoctoral research of Juliana Silva Cassoli and the master’s research of Caroline Brandão Teles, both with scholarships from FAPESP and supervision by Martins-de-Souza.