Scaffold for Core Labs

Scaffold for Core Labs

Designed for Core Labs

If you run a proteomics core facility providing MS/MS protein identification services, Scaffold will make your life easier.

  • Make sense of the proteins identified by SEQUEST® or Mascot®
  • Communicate these results to your customers.

Analyze Data

Scaffold makes sophisticated data analysis easy -—
  • Quickly run a statistical analysis on your SEQUEST® or Mascot® results.
  • Let Scaffold's statistical algorithms automatically adjust for:
    1. the size of the FASTA database searched,
    2. the characteristics of the sample,
    3. the quality of the spectra.
    No tuning required!

Share results

Now it's easy to share MS/MS protein IDs —
  • Put all results from each customer's samples in one file.
  • Control the level of detail your customers will see.
    1. Proteins and samples table
    2. Proteins, peptides and spectra
    3. Statistical justification of algorithms
  • Send result files from Scaffold directly to your customers and collaborators.
  • Tell your customers to get our free Scaffold Viewer to review these results.


Empower customers

The free Scaffold Viewer meets the needs of all core lab customers —
  • The proteins are organized to show at a glance
    • Which proteins are in each sample
    • Which samples are in each sample category
    • How likely the protein is identified correctly
    • How many peptides and spectra support each protein identified.
  • The proteins can be sorted, filtered, validated, and linked to outside databases.

Minimize support time

Your customers will put less demands on you because —
  • They have a viewer on their own computer.
  • They can easily install, learn and use the Scaffold Viewer.
  • They can make their own trade-offs between
    • fewer proteins, fewer false positives
    • more proteins, more false positives.
  • They can export the results.
  • They now own and can archive their own data.
  • They can prepare the figures and graphics needed for publication.

Try Scaffold Today.

For more information see our Scaffold and Scaffold Viewer pages.

  • SEQUEST® is a trademark of the University of Washington and is available from Thermo Electron.
  • Mascot® is a trademark of Matrix Science.

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