Stable isotope labelling experiments such as Icat, the more recently introduced ICPL technology, or even user-defined isotopic labels are fully supported in the new software releases
Bruker Daltonics has launched Proteineer-LC 1.1, describing it as a unique LC-MS/MS-based quantitative proteomics solution, and the new ProteinScape 1.3 release of its bioinformatics software.
Stable isotope labelling experiments such as Icat, the more recently introduced ICPL technology, or even user-defined isotopic labels are fully supported in the new software releases.
The Proteineer software suite extends the existing workflow support from 2D gel to LC-MS/MS based protein identification and quantitation using Bruker Daltonics's Ultraflex II Maldi-Tof/Tof and HCTultra ion trap mass spectrometers.
Proteineer-LC 1.1 now provides the quantitative information associated with protein identification to deliver the desired biological insights, says the company.
As complex protein mixtures are analysed in more and more depth, there is a demand for proteome analyses of increasing numbers of fractions.
The resulting very large amounts of data require database solutions that merge the information and provide powerful data validation tools.
ProteinScape software, co-developed with Protagen, integrates all major search engines including Mascot, Phenyx and Profound.
The unique MetaScore algorithm combines the results from these search engines to increase information readout.
The unique ProteinExtractor algorithm generates true non-redundant protein lists from LC-MS/MS search results.
Both algorithms reduce manual validation efforts significantly.
For in-depth analysis, more detailed protein sequence and modification interpretation is provided by the fully-integrated BioTools protein analysis software for interactive data validation and discovery: PTM and mutation screening, or de novo sequencing combined with homology searches allow the extraction of more information based on sequence annotated data.
LC-Maldi utilises Bruker Daltonics's disposable Prespotted AnchorChips for highest sensitivity, elimination of interfering memory effects and ultimate spot-to-spot quantitation reproducibility.
The Proteineer-LC 1.1 combination of LC-ESI-Maldi into a single workflow allows scientists to validate and complement LC-ESI-MS/MS results with LC-Maldi-Tof/Tof data, says Bruker.
The Proteineer-LC 1.1 Survey Viewer is said to provide a new level of interactive LC-MS and MS/MS data evaluation.
Helmut Meyer, from the Medical Proteome Centre of the University of Bochum, Germany, and coordinator of the Hupo brain proteome project (HBPP), said: "ProteinScape is already used by the HBPP research groups around the globe.
"We are happy to see that a great number of proteomics workflows are now manageable under ProteinScape 1.3.
"Within HBPP, we routinely share data from entire projects within our research network on this bioinformatics platform.
"This enables us to build a data collection centre providing proteomics data to the scientific community via EBI's Pride database".
Herbert Thiele, director of bioinformatics at Bruker Daltonics, added: "We believe the increased functionality and algorithms of our new software suite give researchers options they have been looking for.
"We have collaborated with the Hupo Proteomics Standards Initiative (PSI) since its inception to define community standards for data representation in proteomics, and we fully support the mzData standard in ProteinScape 1.3".
