Bruker Daltonics Introduces Several Important and Novel Proteomics Capabilities and Solutions at HUPO 2007

At the Human Proteome Organisation’s (HUPO) 6th Annual World Congress, Bruker Daltonics is announcing several novel capabilities and solutions for proteomics mass spectrometry at two Bruker luncheon seminars on Monday and Wednesday, as well as in more than 40 scientific oral and poster contributions.

Bruker Daltonics was the first company to introduce ETD (Electron Transfer Dissociation) on its commercial high-capacity trap, and has by far the largest number of successful ETD customer installations. With the release of its new Compass™ 1.3 ion trap software, Bruker’s high-capacity trap HCTultra PTM Discovery System™ becomes the first commercial mass spectrometer fully equipped with both ETD and PTR (Proton Transfer Reaction). Using a unique and innovative ion optics design and chemistry setup for ETD/PTR allows rapid, routine top-down characterization of large peptides and mid-size proteins in the high-capacity ion trap with superior sensitivity.

The usefulness of ETD/PTR is demonstrated impressively by the unambiguous characterization of post-translational modifications. Compass 1.3 also introduces a novel CID fragmentation mode, called PAN™, which eliminates the low mass cut-off of ion traps in MS/MS. It enables multiplexed quantitative proteome analyses by, e.g. iTRAQ™ labelling chemistry, on Bruker’s high-capacity ion trap systems. Moreover, a new AutoMSn mode in Compass 1.3, called “ActiveEjection”, automatically eliminates the most abundant ions in order to further enhance dynamic range. Finally, “Scheduled Target Lists” in Compass 1.3 extend the number of possible MRM transitions per run. This new dynamic scheduling allows monitoring hundreds of target compounds in parallel for large scale biomarker validation studies or for pesticide, drug and doping screening.

With its new ProteinScape™ 2 software, Bruker Daltonics introduces a next-generation bioinformatics platform addressing scientists’ current needs in biomarker profiling, quantification and validation. As a comprehensive solution for qualitative and quantitative LC-MS/MS protein analysis, ProteinScape 2 supports all current label chemistries including multiplexed labels, as well as label-free quantification. Interactive validation of protein quantification based on raw LC/MS data is simple and straight forward. It streamlines the discovery process through decoy auto-validation algorithms and the ProteinExtractor™ algorithm that produces non-redundant protein result lists across entire proteomics projects.

ProteinScape 2 has a number of dedicated data viewers that permit the evaluation and validation on each level of proteomics experiments, such as the LC/MS survey viewer, the gel viewer and sequence-annotated MS/MS spectra. All these views are linked and permit simple browsing through scientists’ proteomics data, supported by extensive queries. It also allows the retrieval of data generated years ago, allowing their joint re-analysis with novel analytic capabilities and mining tools.

Recent data on biomarker discovery, obtained with the Bruker Daltonics MALDI Molecular Imager™ system, demonstrates the power of direct tissue analysis by MALDI-TOF and MALDI-TOF/TOF, such as the ultraFlex™ III TOF/TOF shown here. The complete Bruker solution comprises the new ImagePrep™ device for automated high-resolution matrix application on tissue, the unique SmartBeam™ laser technology and the proprietary ClassImaging™ algorithm for tissue classification and biomarker detection, molecular histology as well as imaging of drug and metabolite distributions in drug development.