Following many months of transporting samples between various collaborators’ facilities in order to perform different experimental steps, Thermo Electron is planning to open a new biomarker facility in Cambridge, Mass., where its own scientists and collaborators can use the company’s proteomics equipment.
According to Leo Bonilla, the head of the new center, the 3,000-square-foot facility will house Thermo-made hybrid LTQ-FT, LTQ-FT, LTQ, and triple quadrupole mass spectrometers; freezers; speed vacs; and a sizable IT infrastructure put together by IBM Life Sciences.
The facility, called the Biomarker Research Initiatives in Mass Spectrometry Center, is slated to open in the beginning of next year
“It will be nice to have one place where you can actually do all the steps of the experiment,” said Bonilla. “Right now we collect at [Massachusetts General Hospital], then we fractionate some of the samples at Bill Hancock’s lab at Northeastern [University], and we also do a lot of the affinity capturing of glycoproteins in his lab. With this new center, the samples will go directly from the freezers at MGH to our freezers in the center.”
It was unclear at deadline how much Thermo will spend on equipping the new center and leasing the portion of the Cambridge building to be used for the center.
In collaboration with MGH and other Boston research institutions, including Harvard medical school, Brigham and Women’s Hospital and Children’s Hospital, Thermo began working on the discovery of biomarkers for cardiovascular disease in 2001. The idea for the center grew out of the cardiovascular research and company initiatives to fund areas of strategic growth.
“Right now we have the best technologies. We need to demonstrate to the marketplace that these technologies bring a lot of added value to clinical proteomics,” said Bonilla. “Working with collaborators on real world samples forces us to take a solution-based approach to biomarker discovery and validation.”
Bonilla said one of the reasons Thermo chose to work on cardiovascular disease as opposed to cancer or another disease is because patient response can be rapidly induced with cardiology in comparison with cancer, which can take years to develop. In addition, MGH has a large number of well-annotated plasma samples from well-characterized clinical trials of patients with cardiovascular disease.
“With work like this, you can’t do it on four, five samples. You need the number and backup of a hospital,” said Bonilla. “In the discovery phase, you need hundreds of patients, and to validate, you need more — closer to thousands of patients.”
According to Bonilla, researchers have found some gold- standard cardiovascular disease markers using Thermo’s biomarker discovery methods. In addition, some new biomarkers that are relevant to the disease have been found. Details of these new biomarkers will be disclosed during a presentation at the Human Proteome Organization conference in Beijing at the end of the month, Bonilla said.
After it identifies biomarkers, Thermo will use funds from several NIH grants collected in a partnership with MGH to validate the markers and take the discoveries to a more clinical setting. Mass spectrometry will primarily be used for validation, along with ELISA immunoassay techniques, said Bonilla.
Working with clinicians is different from working with mass spectrometrists in that clinicians are more interested in getting a statistically validated answer, as opposed to how to get an answer, Bonilla pointed out.
“Clinicians are on a faster track to start answering relevant biological questions,” said Bonilla. “They want to know what the protein is, and how did it change over time?”
Ken Miller, product marketing manager for proteomics at Thermo, said that timing-wise the decision to build the new biomarker center coincided with the introduction of several new instruments that provided better protein coverage, including the Finnegan LTQ ion trap and the Finnegan LTQ-FT.
“Our ability to really couple these new instruments with our expertise and partners all wrapped around the decision to open this new biomarker center,” said Miller.
In preparation for large-scale validation studies, Bonilla said he is currently working with Thermo’s robotics division and with IBM to set up a system for handling thousands of samples per day, and for storing gigabytes of data per day.
“We’re just at the tip of the iceberg. This is the early-discovery phase,” said Bonilla. “We need to expand our findings to a larger training set and after that we need to go to validate these things in a high-throughput fashion.”
The new center is expected to function as one large laboratory used by scientists from Thermo and MGH on a permanent basis, and open to other collaborating researchers on an as-need basis.
The first equipment to the new center is expected to be shipped in a few weeks, Bonilla said, and the lab will be open to select scientists by early next year.