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.

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.

Your customers will put less demands on you because —

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.

1-(800) 944-6027
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