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Bruker Daltonics Introduces Several Proteomics Capabilities and Solutions at HUPO 2007

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At the Human Proteome Organization’s (HUPO) 6th Annual World Congress, Bruker Daltonics is announcing several 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 claims that it was the first company to introduce ETD (Electron Transfer Dissociation) on its commercial high-capacity trap, and has by far the largest number of 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 an ion optics design and chemistry setup for ETD/PTR allows 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 by the characterization of post-translational modifications. Compass 1.3 also introduces a CID fragmentation mode, called PAN™, which eliminates the low mass cut-off of ion traps in MS/MS. It enables multiplexed quantitative proteome analyses 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.

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.

The ProteinScape 2 processing pipeline adopts the "HUPO Brain Proteomics Project processing guidelines" (forum.hbpp.org) and will facilitate the direct submission process of project data adhering to HUPO/PSI publishing guidelines.

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 SmartBeam™ laser technology and the ClassImaging™ algorithm for tissue classification and biomarker detection, molecular histology as well as imaging of drug and metabolite distributions in drug development.