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ASMS Sees Launch of New High

Nov 23, 2023Nov 23, 2023

NEW YORK – At the American Society for Mass Spectrometry annual conference this week in Houston, Thermo Fisher Scientific and Bruker both introduced instruments that could substantially boost the power of proteomic analyses.

The two instruments offer improvements in both throughput and depth of coverage and should address challenges across a range of proteomics applications, including particularly hot research areas like single-cell and plasma-based experiments.

Bruker's new timsTOF Ultra mass spectrometer is the latest edition in its timsTOF line of instruments. These instruments have seen substantial uptake from proteomics researchers since they were first launched in 2016, offering a stiff challenge to Thermo Fisher's Orbitrap technology, which had dominated the space for much of the preceding decade.

Karl Mechtler, proteomics head at Vienna's Research Institute for Molecular Pathology, said the new instrument brought together aspects of Bruker's existing timsTOF SCP, which is intended for the analysis of single cells and other small volume samples, and its timsTOF HT, which is more targeted to deep, high-throughput proteomic analyses of bulk samples including plasma.

The Ultra improves upon the SCP's small sample analysis capabilities, while also allowing for high performance analysis of larger samples, Mechtler said, though he suggested that for particularly complicated samples like plasma the timsTOF HT would likely still be the better instrument.

At this week's ASMS meeting, Bruker highlighted the Ultra's capacity for single-cell proteomics, in particular, noting in press materials that the instrument can identify roughly 5,000 proteins at the single-cell level and quantify more than 4,800 proteins at coefficients of variation of under 20 percent.

Mechtler presented data at Bruker's user meeting this week that his lab had generated using the Ultra instrument. On the Ultra, he and his colleagues were able to measure roughly 6,000 protein groups with a median coefficient of variation of 10 percent in a 250 picogram standard (approximately equivalent to the amount of protein in a single cell) compared to around 5,000 proteins with a median CV of 12 percent using the SCP. Looking at actual single HeLa and K562 cells (as opposed to standards), his lab identified, respectively, 3,803 and 3,221 proteins using the Ultra.

While Bruker's Ultra is an update of an existing platform, Thermo Fisher's new release, the Orbitrap Astral MS, marks the introduction of a new technology, the company's Astral (for asymmetric track lossless) analyzer. Much like a time-of-flight (TOF) analyzer, the Astral measures the travel of ions along a track within the instrument and their arrival at the surface of a detector. However, according to the company, the Astral achieves significantly better ion transmission than a typical TOF instrument, with more than 80 percent of ions reaching the detector. The system uses asymmetric ion mirrors to form an open electrostatic trap, creating a 30-meter-long track for the ions to run along.

The instrument also includes a quadrupole upfront and an Orbitrap analyzer. The Astral analyzer offers a scan rate of up to 200 Hz and resolution of 80,000, while the Orbitrap offers scan rates of up to 40 Hz and resolution of up to 480,000. The Orbitrap's Biopharma Option allows for analysis of molecules of up to m/z 8,000.

Orbitraps provide significantly higher resolution than TOF analyzers. TOFs offer much higher scan speeds, though, and in recent years many proteomics researchers have moved toward these faster instruments. As Ben Orsburn, a proteomics researcher in the department of pharmacology and molecular sciences at Johns Hopkins University and a former senior field applications scientist in proteomics for Thermo Fisher, told GenomeWeb last year, the high speed of TOF instruments like Bruker's timsTOF and Sciex's ZenoTOF made it hard for him to go back to the slower Orbitrap-based instruments.

With its 200 Hz scan rate, the Astral should help Thermo Fisher address this speed gap. By comparison, the ZenoTOF offers a top speed of 133 Hz while Bruker's timsTOF HT, previously the company's top-of-the-line instrument, has a top speed of 150 Hz. Bruker's new Ultra instrument, meanwhile, tops out at 300 Hz.

This speed will prove useful for data-independent acquisition (DIA) workflows, which Bradley Hart, senior director of analytical sciences marketing and life sciences mass spectrometry product marketing at Thermo Fisher, said is a new point of emphasis for the company.

While Thermo Fisher has long developed and offered DIA workflows for use on its Orbitrap-based instruments, Hart said it has traditionally put more resources into workflows using data-dependent acquisition and tandem mass tag labeling.

This, he said, put the company somewhat out of step with certain of its customers and the proteomics space more broadly as DIA workflows grew in popularity.

"It was our miss," Hart said of Thermo Fisher's failure to prioritize DIA workflows. "We sort of believed that DIA had some challenges, maybe it wasn't reproducible, the numbers were all over the place when it came to IDs, and quantitatively [it was] questionable. But I guess our customers proved us wrong in a lot of ways."

This realization led the company to rebuild its DIA offerings, Hart said, highlighting a new DIA setup that combines its Vanquish NEO UHPLC system, µPAC NEO HPLC columns, EASY-Spray Nano Source, and Proteome Discoverer software with the Chimerys search algorithm. This setup is not specific to the Orbitrap Astral, but the instrument shows strong performance when used for DIA workflows. According to Thermo Fisher, it is capable of running DIA experiments using 13.4-minute LC gradients (100 samples per day) that measure more than 8,500 proteins in HeLa cell lysate.

Joshua Coon, professor of biomolecular chemistry and chemistry at the University of Wisconsin-Madison and an early-access user of the Orbitrap Astral, said that using the instrument his lab had measured 8,000 proteins in cell lines and brain cell samples with an eight-minute LC gradient. In another experiment, the lab split those samples into eight fractions, running each using an eight-minute gradient and measured 12,000 proteins in a little over an hour.

"That is, I think, quite remarkable," Coon said. "That means that if you want to do large-scale studies, it really opens the door to have that throughput that you need. We've been getting better [on throughput], but this is a noticeable step up."

Jennifer Van Eyk, director of the Cedars-Sinai Medical Center Precision Biomarker Laboratories, has been using the Orbitrap Astral for plasma proteomic analyses, where it also appears to provide a substantial boost in power over preexisting instrumentation. Van Eyk said that in experiments running 60 samples per day in undepleted plasma, the new instrument is able to measure between 2 and 2.5 times as many proteins as measured using the same workflow on Thermo Fisher's 480 Exploris instrument.

"We're pulling up not just more proteins, but more quantifiable proteins, and proteins that are repeatable, meaning, if we run [a sample] five times, do we see it all five times," she said. "It is a big jump."

Perhaps most impressive is the throughput the instrument enables, Van Eyk said, noting that she and her colleagues have gotten good data and deep coverage running up to 180 undepleted plasma samples per day.

"At 180 samples [per day], all of a sudden you can start talking about running 10,000 samples, and then it becomes a population study," she said.

"We think this instrument has the potential to start to [enable] real high-throughput, big cohort studies for proteomics, finally really getting to precision medicine and personalized medicine," Hart said. He said that in its internal work, the company had shown the instrument can measure roughly 600 proteins in undepleted, unfractionated plasma samples when running them at a rate of 180 samples per day.

Fractionating and enriching plasma samples allows the instrument to go much deeper. Hart said that with Seer's Proteograph platform, which uses nanoparticles to enrich plasma samples for proteomic analyses, the Orbitrap Astral is able to measure roughly 6,000 proteins in plasma with a throughput of four samples per day. That throughput should increase with the recent release of Seer's new version of its Proteograph assay kit, the Proteograph XT. While the original kit required that users split their samples into five fractions, meaning each sample required five separate LC-MS runs, the XT requires only two fractions, meaning each sample requires just two separate LC-MS runs. In data Thermo Fisher showed this week at ASMS, the Orbitrap Astral was able to measure roughly 6,000 proteins in around 30 plasma samples per day using the new XT kit.

Coon, who is a user of Seer's Proteograph platform but has not yet used it with the Orbitrap Astral, also cited the instrument's strong performance in plasma, noting that his lab was able to measure roughly 1,500 proteins in undepleted, unenriched plasma using a 50-minute LC gradient and had developed a one-minute direct infusion method on the instrument capable of measuring around 200 proteins per sample.

Coon said that while "mass spec launches often tend to be real but modest boosts," he viewed the Orbitrap Astral as a more dramatic advance. "I think it's a big deal."

The plasma proteomic data generated on the Orbitrap Astral "is really spectacular," Mechtler said, though he noted that it remains to be seen how well it holds up once the instrument is in broader use. He also said that the data he has seen for single-cell experiments indicates that the Ultra is the better performing system in this regard, offering reproducible quantitation for a larger number of proteins.

"The two machines are both really spectacular," Mechtler said. "I wouldn't say 'buy this machine, or buy this machine.' Both are really great."