After years of technical setbacks and challenges, mass spec-based clinical proteomics is "ready for prime time," a Thermo Fisher Scientific researcher told ProteoMonitor this week.
Discussing a recent paper in Clinical Biochemistry detailing a series of protein quantitation assays developed and run using the company's mass spectrometric immunoassay technology, Mary Lopez, director of Thermo Fisher's BRIMS Center, said that "the throughput and quality of the data" generated by the technology "are ready to be put to the test."
"This paper was really about kicking the tires as hard as we could with a wide variety of analytes and a wide variety of situations to see if we could break it," she said. "And we have not to date been able to break it."
As Lopez went on to note, "clinical research is a very conservative world" and it will no doubt still take considerable time, money, and effort to establish mass spec-based proteomics as a routine clinical tool. However, her comments, along with several other recent developments, suggest that the field may have turned a corner in terms of achieving technical feasibility.
Two years ago this week at the 2011 Mass Spectrometry's Applications to the Clinical Lab meeting, SISCAPA Assay Technologies CEO Leigh Anderson gave a talk in which he lamented the low throughput of mass spec-based proteomics, asserting that without gains in this area the technique would never prove a useful clinical tool (PM 2/11/2011).
"I'm a little bit embarrassed to say that in the 5,000 or 10,000 papers on biomarker proteomics, I don't know of a single one in which anybody has actually run 1,000 samples," he said at the time. "And it's well known in the diagnostics community that if you can't run a few thousand samples, you can't know if a biomarker is clinically relevant. So this is a huge limitation that we need to overcome. Robustness and automation are becoming major barriers to applying this kind of [proteomic] methodology to solving our problems."
Since then, however, advances in sample prep automation and reproducibility, target enrichment workflows, chromatography speed, and mass spec sensitivity have pushed the technology ever closer to Anderson's stated goals.
In the Clinical Biochemistry study, Lopez — along with her Thermo Fisher colleagues and researchers at the University of Gothenburg, Toronto's University Health Network, and King's College Hospital, London — presented mass spec assays in human plasma and serum for sixteen clinically relevant proteins, including members of the apolipoprotein family, parathyroid hormone, prostate-specific antigen, and amyloid beta.
The researchers demonstrated the ability of the MSIA system – which uses a pipette immunoenrichment technology to isolate low-abundance proteins in complex samples – coupled to selected-reaction monitoring mass spec on a Thermo Scientific TSQ Vantage instrument to quantify target proteins at levels as low as the picograms-per-milliliter range and with interlab coefficients of variation of under 20 percent.
The assays required roughly five to seven minutes of LC-MS run time for each sample, allowing for processing of 200 to 300 samples per instrument per day – a number, Lopez noted, that could be increased by multiplexing the chromatography.
Lopez presented on these ApoE and A-beta assays and their potential as Alzheimer's biomarkers this week at the Uppsala Diagnostics Forum. One of her co-authors, University of Gothenburg researcher Erik Portelius, told ProteoMonitor that these assays appeared to offer a significant improvement over existing methods, particularly given that they were measuring the proteins not in cerebrospinal fluid, but in plasma.
"The level of A-beta in plasma is roughly 50 picograms per milliliter," he said. "So it's a very sensitive method to detect it with mass spec. It's very good work."
Portelius, who specializes in Alzheimer's research, did not work on the assay development portion of the study, but collaborated with Lopez and Thermo Fisher on implementing their assays in clinical samples. He now plans to use the technique to look at different isoforms of A-beta in the plasma of Alzheimer's patients to see if any add diagnostic information to that offered by A-beta42, the isoform form most commonly used as an Alzheimer's marker.
The Clinical Biochemistry work is one of several recent publications that suggest the clinical suitability of mass spec-based protein quantitation. For instance, in November, researchers from SAT and Agilent published on a selected-reaction monitoring mass spec-based peptide quantitation workflow with a sample cycle time as short as seven seconds (PM 11/16/2012), the most recent product of several years of collaboration between Agilent and SAT's Anderson on clinical mass spec workflows.
And, at this week's MSACL annual meeting, Anderson presented data demonstrating that he and his colleagues are able to bring CVs for trypsin digestion down into the 2 to 3 percent range, enabling highly reproducible protein quantitation.
Also at MSACL, several mass spec vendors issued news and product announcements indicative of a continued push toward clinical proteomics.
Thermo Fisher launched its new Prelude SPLC automated sample prep and LC system, a platform that Lopez said is "designed for high-throughput clinical applications … and would be absolutely compatible with the [MSIA-SRM] workflow."
"As the clinical research community increasingly recognizes the benefits of LC-MS/MS, we set a goal to make this technique more accessible than it is with standard HPLC systems," Ken Miller, Thermo Fisher vice president of marketing for life sciences mass spectrometry, said in a statement accompanying the release of the device.
AB Sciex, meanwhile, released two new LC-MS/MS systems – the AB Sciex API 3200MD and 3200MD QTRAP – that it has registered with the US Food and Drug Administration as Class I exempt medical devices and is marketing for use as in vitro diagnostic devices.
"Clinical diagnostics is the new frontier for mass spectrometry," AB Sciex president Rainer Blair said in a statement. "The introduction of the 3200MD series is a major milestone for AB Sciex itself in response to the demand in clinical settings for mass spectrometers as medical devices that meet regulatory requirements."
And Agilent this week said that it has entered into a strategic partnership with proteomics firm Sera Prognostics to help it develop mass spec assays for its ProNid protein biomarker-based test for predicting preterm birth risk.
This is the latest protein assay development deal for Agilent, which, via this agreement and a collaboration announced last year with Integrated Diagnostics (PM 1/13/2012), has placed itself at the forefront of mass spec-based clinical proteomics.
Both InDi and Sera plan to bring mass spec-based proteomic tests to market this year. If they are successful, they will be among the first to commercially launch such products. Several proteomics-based diagnostics, including Vermillion’s OVA1, Healthlinx’s OvPlex, and Crescendo Bioscience’s Vectra DA, have gone to market in recent years, but these all use an immunoassay platform, not mass spec. Biodesix’s VeriStrat lung cancer diagnostic runs on a MALDI-MS platform, but relies on comparisons of broad proteomic profiles rather than mass spec measurements of discrete proteins, as the InDi and Sera tests plans to do.
Agilent's primary role in the Sera collaboration will be "to supply equipment and… help the Sera team develop the overall sample-to-analysis workflow," Yvonne Linney, vice president general manager of the company's life science solutions division, told ProteoMonitor via email.
As part of the deal, Sera has purchased multiple Agilent 1290 Infinity UHPLC systems, 1260 Infinity LC systems, and 6490 iFunnel triple quadrupole mass spec instruments. The company also plans to use Agilent's AssayMAP Bravo solid phase extraction and RapidFire chromatography products.
Such collaborations, Linney said, are key to Agilent's efforts to push its mass spec instruments into the clinic for protein quantitation.
"Collaborations like this are very important to Agilent," she said. "We see a growing opportunity for mass spectrometry in the clinical market, and we have all the tools to enable clinical laboratories to develop assays on the Agilent platform in an efficient manner."
Thermo Fisher's Lopez likewise cited such collaborations as the primary route to the clinic for her company's mass spec tools and workflows, now that they appear – as she put it – "ready for prime time."
"We have been promoting this platform, but rather than do kind of a big marketing blitz, we've taken the approach of going to these key opinion leaders and engaging them," she said. Clinical researchers "are not going to look at a glossy brochure. They are going to want to see the results and the data in their own hands."