Arnaud Droit is Associate Professor at Université Laval and director of the Bioinformatics and Proteomics platforms at the Centre de Recherche du CHU de Québec – Université Laval. He is an expert in the development of statistical models and robust methods for extracting information on biological mechanisms from complex omics datasets, statistical and machine learning approaches.
Florence Roux-Dalvai is Research Assistant and Project Manager on the Proteomics platform of Centre de Recherche du CHU de Québec – Université Laval. She is an expert in proteomics and mass spectrometry. She has more than ten years of experience with Orbitrap instruments and used them for deep proteome analyses of complex biological samples.
Arnaud and Florence work together on the development of new approaches combining proteomics and artificial intelligence for the detection of microorganisms in biological fluids.
Continue reading for the interview with Arnaud and Florence.
Q: How did you get involved in bacterial identification & why does it fascinate you?
Florence: Our lab is part of the Quebec City Hospital Research Center and for many years, we have collaborated with researchers from the Infectiology Research Center located in the same building as us. Our discussions with microbiology experts made us think that the diagnosis of bacterial infections, which is currently done using MALDI-TOF mass spectrometry, could be greatly improved. The MALDI-TOF MS-based approach requires a long culture step (24-48h) prior to analysis and during this time, patients receive broad-spectrum antibiotics which are known to strongly increase bacterial resistance in the whole population. Moreover, MALDI-TOF MS is not quantitative and not specific for some bacterial species or subspecies.
We had the idea to combine our complementary expertise — Bioinformatics for Arnaud and Proteomics for Florence — to move the bacterial infection diagnosis a step forward. Thus, we developed a new, recently published strategy that combines LC-MS and artificial intelligence to get ultrafast identification of bacterial species in urinary tract infections.
This collaboration has been very exciting for us since we can see real-world application of our modern technologies in a clinical context. Moreover, fast diagnosis strategies are essential to avoid over-prescription of antibiotics and thus fight against bacterial resistance which can be considered our next global challenge. If nothing is done, antimicrobial resistance could lead to millions of deaths and cost billions of dollars in the upcoming decades.
Q: What type of work have you been doing in the past?
Florence: I have been working with mass spectrometry for more than 15 years. I had the opportunity to work with almost all generations of hybrid Orbitraps, from the very first Thermo Scientific™ LTQ Orbitrap™ MS to the new Thermo Scientific™ Orbitrap Exploris™ 480 mass spectrometer. So, I can really appreciate the improvements in the technology over the years and use it to go deeper into the analysis of complex proteomes, initially in cancer research and now in microbiology research. Recently, the use of data-independent acquisition (DIA) with Orbitrap instruments allowed a breakthrough in our projects where we try to identify low abundant bacterial proteins in large background of human proteins. This type of analysis becomes more and more efficient as soon as the resolution of the instrument is increased without compromise to the Orbitrap scanning speed.
Like what you are learning?
Arnaud: A large part of my career was dedicated to bioinformatic analysis of genomics data. The emergence of next-generation sequencing technologies has recently pushed biology into the world of big data and we had to develop new strategies, including the use of artificial intelligence. We can see now that proteomics is following the same path. The large amount of data produced by the latest mass spectrometers requires the adoption of methods initially developed for genomics being used with proteomics data.
Q: Why did you decide to evaluate the Orbitrap Exploris 480 MS?
Florence: The method we have developed uses proteomics data acquired on the Orbitrap instrument and a machine learning algorithm to identify a peptidic signature that can be monitored on any type of instrument by targeted proteomics. However, monitoring several dozens of peptides requires a certain amount of time to obtain a resolved chromatographic peak for each peptide. We have been able to decrease this analysis time to 30 minutes but in order for the method to be implemented in routine laboratories as a high throughput approach, the analysis time needs to be even shorter. By using DIA analysis on an Orbitrap instrument, instead of targeted analysis, we expect the analysis time to be even shorter, around 5 to 10 minutes. To achieve this goal, we need to perform our analyses on high-performance instruments combining high sensitivity, high resolution and high scanning speed such as the Orbitrap-based mass spectrometers. The Orbitrap Exploris 480 MS fulfills these criteria and we had the chance to collaborate with Thermo Fisher Scientific scientists from Bremen and San Jose to evaluate our methods on this instrument.
Q: I have to ask, is the Orbitrap technology living up to your expectations?
Florence: In general, the quadrupole-Orbitrap hybrid instruments are very well suited for DIA analysis. The high selectivity of the quadrupole in combination with the high resolution of the Orbitrap analyzer is the ideal combination to obtain high-quality MS2 spectra from which we search for bacterial signal using machine learning algorithms. However, the only limitation of these early generation quadrupole-Orbitrap instruments was the scan rate, which limited the number of DIA windows that we could acquire in a chromatographic cycle time. Now, with the new generation of ultra-high-field Orbitrap instrument, we can scan all along the mass range without the need to extend the DIA windows size and avoid increasing the spectrum complexity.
Moreover, the robust and easy-to-use Orbitrap Exploris 480 MS is an ideal instrument to demonstrate that our methods could be applied to high throughput analyses in routine laboratories.
Q: What do you think the future holds?
Arnaud: We both believe that it is only the beginning in the use of artificial intelligence in proteomics but also in clinical research diagnosis. The rapid advancements in mass spectrometry and bioinformatics will help us tackle the complexity of biology and to search for minor changes that can have a strong impact on our health. The fast and accurate detection of microorganisms in clinical samples is still a challenge along with the detection of bacterial resistances, but we think that the combination of these new technologies will be a key solution to address the huge problem of antimicrobial resistance.
Q: You seem to be having fun with the Orbitrap technology, how do you relax away from work?
Florence: We work in a very motivating environment with talented and dynamic people having complementary knowledges. This makes us happy to come to work every day. Of course, as everyone, we like to relax with our friends and families, but the nice atmosphere in our team makes it so that we also like to have fun all together, out of the lab. We like to organize outdoor activities such as hiking or skiing, and then enjoy the beautiful natural surroundings of Quebec City.