Three new Bruker instruments installed at NAPI proteomics core facilities
The NAPI core facilities at Oslo University Hospital, University of Oslo, and the Norwegian University of Life Sciences (NMBU) each received cutting-edge new mass spectrometers from Bruker Daltonics in January/February 2021.
The timsTOF FleX at PCF-OUS. Photo: Sachin Singh
Fundamental challenges in mass spectrometry (MS)-based proteomics include high sample complexity, large dynamic range in protein concentration, and computational analysis of the large and complex data files generated by mass spectrometers.
In recent years, developments in MS instrumentation and analytical techniques have addressed many of these challenges. Advances in mass spectrometers continue to push higher sensitivity, faster sequencing speed and larger peak capacity.
The very latest technology available at NAPI
Thanks to funding from the Norwegian Research Council, the NAPI core facilities at Oslo University Hospital (PCF-OUS), University of Oslo, and NMBU have each recently received state of the art new instruments from Bruker Daltonics. The new mass spectrometers represent the very latest technology available in the proteomics field today, and will greatly expand the analytical capacity of all three NAPI core facilities. This means users can perform more advanced and complex analytical approaches that are required for certain challenging projects, and also benefit from deeper proteome coverage of samples during more standard ‘shotgun’ proteomic analyses.
The timsTOF Pro (University of Oslo and NMBU) and timsTOF fleX (Oslo University Hospital) both make use of an additional dimension of gas phase ion separation via trapped ion mobility spectrometry (TIMS) coupled to ultra high resolution-QTOF technology. This results in the transition from ‘conventional’ 3D-Proteomics (based on retention time, m/z and MS/MS fingerprint) into 4D-Proteomics™ (the addition of peptide separation as a function of ion mobility).
Video: Bruker Daltonics
Advanced speed, sensitivity and spectral quality
Using a technique called parallel accumulation serial fragmentation (PASEF), the timsTOF instruments exhibit advanced speed and sensitivity along with very high spectral quality. This means researchers can dig deeper into their samples in less time, and provides more confidence in the collected data.
You can read more about the timsTOF/PASEF technology on the timsTOF Pro section of our MS instruments webpages.
In addition to advanced MS instrumentation, the timsTOF platform also incorporates new nanoElute high performance liquid chromatography (HPLC) for reproducible separation of peptides prior to injection into the mass spectrometer. This means improved reproducibility between e.g. technical repeat injections of the same sample, and therefore more accurate, higher confidence data.
Discussing the timsTOF Pro and the benefits it brings to NMBU, core facility leader Dr Morten Skaugen said:
"The timsTOF Pro is a high performance instrument that will allow us to explore exciting new applications. The timsTOF instruments from Bruker are also highly robust, allowing for sustained MS performance over larger numbers of samples. The instruments therefore require less ‘downtime’ for fixing technical problems, which means more machine time goes towards sample analysis".
Bernd Thiede, Head of the proteomics core facility at UiO/IBV, added:
“As a core facility we would like to provide the best service possible for our customers. The timsTOF Pro is a state-of-the art instrument with high acquisition speed which allows us to perform proteome analyses much faster and more comprehensively. Witihin NAPI, our facility has a focus on the identification of post-translational modifications (PTMs), and the timsTOF Pro will enable us to study such modifications in a much deeper way”.
Deeper metaproteomic analyses
Dr Magnus Arntzen at NMBU frequently uses proteomics in his research. Discussing the benefits of the timsTOF pro for his specific field, Dr Arntzen said:
“One of our key research topics at the NMBU-NAPI node is metaproteomics; the proteomics of complete microbial communities. This entails detecting microbes, reconstructing their individual metabolisms (in combination with metagenomics) and visualizing the enzymes and pathways active within communities. We are very excited to start using the new TimsToF Pro, which will allow us to dig even deeper into the proteomes of microbial (and host) communities, and even better understand who is there, what they are doing and the level of interplay, e.g. competition and altruism”.
timsTOF fleX for imaging MS
Whilst both the fleX and the Pro instruments possess an electrospray ionisation (ESI) ion source that is most commonly used for LC-MS/MS, the fleX is also equipped with a matrix-assisted laser desorption/ionization (MALDI) ion source.
This enables ‘imaging mass spectrometry’, where the label-free mapping of various target compounds on tissue extracts can be assessed.
At NAPI, we aim to develop imaging mass spectrometry as a future service at the University of Oslo, and you can learn more about this technique on the timsTOF fleX section of our MS instruments webpages.
Discussing the arrival of the timsTOF fleX in Oslo, Head of the PCF-OUS facility Tuula Nyman said:
“At NAPI, we have a focus on clinical proteomics, and the timsTOF flex provides an ideal opportunity for LC-MS/MS-based clinical studies. We are very excited to get started with imaging MS and establish this as a new application within the Norwegian proteomics community. I envisage that this will be an important clinical application in the future, for example to complement immunohistochemistry-based pathology diagnostics”.
Video: Bruker Daltonics
Visit the Bruker website to learn more about the timsTOF Pro and timsTOF fleX. The Bruker website also provides more information on 4D-proteomics and MALDI-guided imaging mass spectrometry, including potential applications for these technologies.
If you are interested in performing mass spectrometry/proteomics experiments for your research project, contact the NAPI Administrative Manager or one of core facilities. Contact details are available on our contacts page.