SORCERER™ 2 Integrated Data Appliances(IDA) for Proteomics Analysis

Sorcerer IDAs (integrated data appliances) provide "plug-and-play productivity" in protein identification using shotgun proteomics, with increased accuracy and throughput, and reduced IT maintenance. The server version, the Sorcerer 2 IDA, is designed to support multiple research groups, such as in proteomics core facilities. It is for researchers whose throughput and sophistication needs outgrow their basic all-in-one PC proteomics software, while offering improved reliability and operating cost compared to cluster computers.

The key benefits of the Sorcerer 2 are

• High throughput
• No IT maintenance
• Plug and play setup
• Simple operation
• Multi-user, webbased access
• Supports all major mass spec vendors
• Search RAW files directly
• Optimized for PTM searches
• Automated false positive estimation
• Data repository

High-throughput, easy to use

The Sorcerer 2 IDA is a fully integrated system that is small enough to fit on a desktop, yet powerful enough to be the main system to run multiple search engines (SEQUEST®, X!Tandem, and optionally PHENYX®) for results analy- sis in Scaffold, the Trans-Proteomics Pipeline or Bioworks®. It increases your productivity with: search speeds of thousands of spectra per hour, in- cluding modifications; the increased accuracy from multiple search en- gines; and comprehensive support through our Total Support Program that can act as your personal infor- matics team. Sorcerer 2 is securely accessible over the network by multi- ple groups. With automated raw file searching and patent-pending index- ing acceleration of SEQUEST searches, Sorcerer 2 makes proteomics data analysis quick and easy.

Specifications

• Compact deskside packaging in quality metal chassis
• External dimensions: 24.6” H × 8.3” W × 24.3”D (617×210×650 mm)
• Standard power outlet – 120/220V autosensing
• Single or available dual Pattern Match Accelerator™
• Enhanced dual-CPU/quad core system processing unit
• 1.5 Terabyte high capacity disk storage (7×250 GB with RAID-5) redundant data technology for results archiving
• Network: Dual port 10/100/1000 Ethernet with TCP/IP automatically configured using DHCP
• PTM-enhanced Sorcerer-SEQUEST peptide ID
• Scaffold Batch protein ID with automated Sorcerer postprocessing
  • Easy results interpretation
  • X!Tandem searching of Sorcerer results
  • Free viewer available to all network users
• Optional Phenyx® protein identification package
• Sorcerer Proteomics Edition application software, including Sorcerer Web Graphical User Interface and embedded RDBMS
• Pre-integrated Trans-Proteomic Pipeline tools (from ISB)
• Multi-vendor instrument support
  • mzXML vendor-neutral format
  • Supports .dta/.out and SRF (Bioworks) formats
  • RAW files (requires separate Xcalibur library installation)
  • .pkl and .mgf for Waters, Bruker and Agilent connectivity

The intuitive Sorcerer PE software offers different workflows for searching your data and viewing your
results. The figure shows the summary view of Scaffold (left), which is ideal for interactive visualization and comparison of experiments , and two tools (right and below) of ISB’s Trans-Proteomic Pipeline.

Phenyx

Phenyx is a software platform for the identification and characterization of proteins and peptides from mass spectrometry data. Developed by GeneBio in collaboration with the Swiss Institute of Bioinformatics (SIB) and 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 results assessment.

Sage-N Research, Inc. (Sage-N) distributed GeneBio's Phenyx platform together with Sage-N's Sorcerer(TM) 2 IDA (Integrated Data Appliance) and as a standalone product as well.

Scaffold

Scaffold complements Sorcerer. High throughput confident protein identification is a two step process. First Sorcerer runs Sequest to match mass spectra to proteins. Then Scaffold validates these protein identifications. Scaffold first automatically validates Sequest results with the "prophet" statistical algorithms and by optionally cross checking Sequest with X! Tandem. Sage-N Research has bundled this part of Scaffold into their Sorcerer Integrated Data Appliance (IDA).

The automatically validated results can be distributed to collaborators who can do further validation manually with the free Scaffold Viewer. Scaffold Viewer provides a variety of ways of focusing the manual validation effort where it is most needed. The validation tactics available include visually checking for repeatability of the proteins across samples, peptides across samples, and the spectral fragmentation peaks across peptides. A more detailed tactic is to verify that the peptide is consistent with the fragmentation peaks in the spectra.

Scaffold complements Sorcerer by validating, organizing, visualizing, and publishing Sorcerer's data. Together Sorcerer and Scaffold provide a complete solution to MS/MS data analysis. Sage-N Research distributes Scaffold as an integrated part of Sorcerer 2.