Bruker Daltonics ProteinScape

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract ProteinScape is an advanced database system for proteomics project management. The ProteinScape database organizes all relevant data for large proteomics projects - including gel data, mass spectra, process parameters, and search results. It supports both, Gel based proteomics and liquid chromatography (LC)-based proteomics workflows like two dimensional- liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS), Liquid chromatography-electrospray ionisation (LC-ESI), LC-matrix-assisted laser desorption/ionization (MALDI) as well as Quantitative Proteomics.

While designed for high-throughput operation, it also provides unique tools that can significantly enhance the results obtained from smaller numbers of samples. To enable automated analysis, ProteinScape has been designed in a way that provides much more than a simple database. Apart from data storage and retrieval, ProteinScape handles the automatic processing of data within the database and interactions with other programs (e.g. database search engines).

Search engines -- Inviting users to process their data using whatever search software they prefer, ProteinScape offers the option to cross- validate or consolidate the identification results through the complementary use of several software packages. For optimization and validation of individual search results the MetaScore algorithm in ProteinScape provides reliability by the intelligent combination of scoring schemes from different search engines.

Improving the Protein Identification Rate -- ProteinScape uses the ScoreBooster feature to improve database search results. Automatic iterative recalibrations and background eliminations by peak rejection technologies are carried out by ScoreBooster technology.

Non-redundant Protein Lists -- To minimize the overall work-load in data evaluation, the new algorithm ProteinExtractor generates true non- redundant protein lists from MS/MS search results, determining which protein variants are contained in the biological sample with the highest probability. The ProteinExtractor decreases significantly, redundancies in the protein lists from search engines.

BioTools Integration -- Detailed data interpretation in ProteinScape is provided by the full integration of BioTools - the protein/peptide data analysis package for interactive work. The BioTools software allows Not only the judging of the correctness of assigned peptide sequences but also provides tools for structure analysis such as mutations, polymorphisms, screening for chemical or post-translational modifications (PTMs), and de novo sequencing (RapiDeNovo). The complete set of new assignments is archived in ProteinScape.

Quantitative Proteomics -- Quantitative comparisons are of growing interest in proteomic research, which is focused on by ProteinScape. The software provides sample comparison tools for label-free as well as stable-isotope labeling methods. Per default, all relevant labels [Isotope Coded Protein Labeling (ICPL), Isotope Coded Affinity Tags (ICAT) etc.] are available, and new or customized labels can be defined. The integrated algorithms for quantification are applicable to both types of MS techniques: ElectroSpray Ionisation-Ion Trap (ESI-IT) and MALDI TOF-Time of Flight (TOF).

mzData Standard -- Automation, integration and standardization are the driving forces in bioinformatics for proteomics. Bruker Daltonics has collaborated with the HUPO Proteomics Standards Initiative (PSI) since its inception to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. By adding the mzData standard to ProteinScape the user gets greater flexibility to share data more easily which greatly accelerates the process of extracting knowledge from the experimental data.

A unique database for heterogeneous proteomics data -- ProteinScape is the bioinformatics backbone of the HUPO Brain Proteomic Project (HBPP). ProteinScape is used at the HBPP's data collection center (DCC) to centrally process HUPO project data that were obtained from researchers from all over the world with a variety of workflows and mass spectrometers.

Additional features/capabilities include:

1) Storage of all sample and project relevant data (sample pre- treatment, gel images, peak lists, search results, etc.).

2) Intelligent result(s) feedback (WARP) for the definition of MS/MS work lists to make most efficient use of the equipment.

3) Gel image based handling of data for visualization and information retrieval.

4) Advanced tools for hit validation (easy visualization for ion series annotations, metascores for the results combined from different database search engines etc.).

5) Advanced data reporting tools (Gelviewer Pack&Go) for sharing results with others, plus easy data transfer into Excel or PowerPoint.

6) Unlimited database size (>1 million spectra is possible).

7) MALDI and ESI data from all Bruker instruments is handled.

8) Data importing capabilities for various external data formats.

9) Support of FASTA formatted protein databases.

10) Interface to Phenyx (see G6G Abstract Number 20080), a software platform for the identification and characterization of proteins and peptides from mass spectrometry data. Incorporating the true probabilistic and flexible scoring system OLAV, Phenyx is specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic high quality results assessment.

11) Support of different search engines: MASCOT (see G6G Abstract Number 20087), Phenyx, ProFound, Sonar, MS-Fit and Sequest.

System Requirements

* Relational database system based on Microsoft SQL

* Operating system Microsoft Windows 2000, Internet Explorer 6.0 compatible

* N-tier client-server architecture, providing maximum flexibility in configuration

* Web-based platform with Intranet and Internet capability

* Communication with all PROTEINEER hardware and software components via XML

* Multi-user, multi-process capability


Manufacturer Web Site Bruker Daltonics ProteinScape

Price Contact manufacturer.

G6G Abstract Number 20079

G6G Manufacturer Number 100442