In another sign that Bruker Daltonics’ MALDI TOF-TOF mass spectrometer may be beating out Applied Biosystems’ version of the instrument, Roche said last week that as part of a technology development agreement it intended to trade in at least 10 of its 12 Bruker-built MALDI TOFs for next-generation Bruker TOF-TOFs over the next year.
Bruker and Roche have worked together on a preliminary basis for three years, but last week’s announcement cemented their relationship, giving Bruker rights to commercialize any products that arise from the collaboration, and setting a goal of creating a mass spectrometer capable of analyzing 10,000 proteins per day.
More than a deal to negotiate a lower price on the instruments, “it’s really a strategy to develop technologies together,” said Hanno Langen, head of proteomics at Basel, Switzerland-based Roche. “For us the most important thing is automation aspects in mass spectrometery.”
But the fact that GeneProt, and now Roche, have opted for the Bruker version of the TOF-TOF technology may indicate that there are differences between the instruments that transcend historical relationships between users and manufacturers. Langen said he was not familiar with the latest version of ABI’s technology, having looked at its TOF-TOF instrument two or three months ago, but that at the time the major advantage for Bruker was that it was “completely integratable in a high-throughput setting because they have the microtitre plate format.”
Another benefit to Roche is that the deal with Bruker provides, in addition to price discounts on mass spectrometry equipment, free use of any technology that Bruker comes up with during the course of their work together.
New Bruker MS Software
Already Bruker is preparing to release a new version of a software and database product in several weeks that would automate mass spectrometry data acquisition, assign masses to peaks, sift through the data to recognize true monoisotopic peaks, and store mass spec results along with associated proteins’ 2D gel images and amino acid sequences.
However, the product, called ProteinScape, will not automatically search protein sequence databases to match up peptide fragment ions with their respective database sequences, said Detlev Suckau, a MALDI application development manager at Bruker in Germany. Instead, users rely on commercially available software from companies such as Matrix Science.
The Roche collaboration presented a good opportunity for Bruker to work with researchers generating such large amounts of mass spectrometry data, added Suckau. “They have a need for reliable data automation,” he said, “and we expect more customers to also have this demand.”
To build an instrument platform capable of collecting data on 10,000 proteins per day, Bruker and Roche also intend to continue boosting throughput from the sample preparation side, Suckau said. Roche has already integrated Bruker’s Anchorchip technology for reducing the size of spots on the MALDI plate, which in theory allows researchers to analyze more proteins at once, while also increasing the size of the “sweet spot” on the MALDI target, he added.
Although Roche works primarily with proteins excised from 2D gels, Langen said his group is also using chromatography techniques combined with LC/MS/MS systems. In addition to MALDI instruments from Bruker, his group operates, QSTAR Q-TOF instruments from MDS Sciex, and DECA ion traps from Thermo Finnigan.
Langen added that his group has also studied combining chromatography separation with the MALDI mass spectrometers. “We are pretty much independent as to what instruments we use, and also which type of technology we use,” he said. “But our main focus is on the 2D gel separation because we still believe it’s the best separation technology around for proteins.” — JSM