ProteinScape

The ProteinScape™ database organizes all relevant data for larger proteomics projects - including gel data, mass spectra, process parameters, and search results.

It supports both, Gel based proteomics and LC-based proteomics workflows like 2D-LC-MS/MS, LC-ESI, LC-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 the 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 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 highest probability. The ProteinExtractor decreases significantly redundancies in the protein lists from search engines – formerly a tedious time-consuming work.

BioTools Integration

Detailed data interpretation in ProteinScape is provided by fully integration of BioTools™ – the protein/peptide data analysis package for interactive work. The BioTools software allows not only judging the correctness of assigned peptide sequences but also provides tools for fine structure analysis such as mutations, polymorphisms, screening for chemical or post-translational modifications, and de novo sequencing (RapiDeNovo). Finally the complete set of new assignments are archived into ProteinScape to keep track of the project.

Quantitative Proteomics

Quantitative comparisons are of growing interest in proteomic research, which is focused by ProteinScape. The software provides sample comparison tools for label-free as well as stable-isotope labelling methods. Per default, all relevant labels (ICPL, ICAT etc.) are available, and new or customized labels can be easily defined. The integrated algorithms for quantification are applicable by both types of MS techniques: ESI-IT and MALDI TOF-(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 comparision, exchange and verification. By adding the mzData standard to ProteinScape the user gets a great flexibility to share data more easily which greatly accelerates the process of extracting knowledge out of the experimental data.

A unique database for heterogeneous proteomics data

ProteinScape is the bioinformatics backbone of the HUPO Brain Proteomics Project. 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.

Features of ProteinScape

• Full support of Gel based proteomics and LC-based proteomics workflows: 2D-LC-MS/MS, LC-ESI, LC-MALDI.
• Quantitative proteomics: Label-free, SILE (e.g. ICPL, ICAT).
• Seamless link of MS and MS/MS spectra and web-based library searches.
• Storage of all sample and project relevant data (sample pre-treatment, gel images, peak lists, search results, etc.).
• Automatic database searches using different search engines and different search strategies in parallel.
• Optimization and validation of individual search results through MetaScore algorithm.
• Intelligent result feedback (WARP) for the definition of MS/MS worklists to make most efficient use of the equipment.
• Unique ScoreBooster technology to improve MS fingerprint search results.
• Gel image based handling of data for visualization and information retrieval.
• Advanced tools for hit validation (easy visualization for ion series annotations, metascores for the results combined from different database search engines etc.).
• Advanced data reporting tools (Gelviewer Pack&Go) for sharing results with others, plus easy data transfer into Excel or Powerpoint.
• Unlimited database size (>1 million spectra is easily possible).
• MALDI and ESI data from all Bruker instruments is handled.
• Data importing capabilities for various external data formats.Support of FASTA formatted protein databases
• Interface to Phenyx, 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.
• Support of different search engines: MASCOT, Phenyx, ProFound, Sonar, MS-Fit and Sequest.
• BioTools 3.0 integration for interactive validation.
• Support of mzData standard, developed by the HUPO Proteomics Standards Initiative.

Technical Data

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