Software at the APL

Our 4700 Explorer software allows acquisition of MS and MS/MS spectra on a high-throughput MALDI platform. The spectra are stored in an Oracle database, rather than separate files for each experiment, individual spectra can be exported as *.T2D files and opened by Data Explorer.

The software we use for extensive Mascot integration is called GPS Explorer. Search parameters are defined as part of an Analysis in GPS Sample Setup. On completion of each search, the results are imported into the 4000 series database and can be viewed and reported using the GPS Results Browser. The workflow supports both ICAT® and iTRAQ™ quantitation.

The easy-to-use interface enables quick and efficient acquisition, data processing and results delivery. Xcalibur integrates instrument setup, acquisition, data processing and reporting. Results can be quickly reviewed with the Qual, Quan and Library Browsers. BioWorks combines with XCalibur as an application for protein identification and quantitation featuring the Sequest search algorithm.

This piece of software combines and validates results from multiple search engines (Sequest, Mascot and X!Tandem) to increase coverage and confidence, to visually compare results across an entire experiment. Scaffold also allows the organization and sharing of significant MS/MS data with clients and colleagues. Scaffold viewer allows viewing of any data loaded and analyzed by Scaffold.