Scaffold Q+ for Proteomics

Scaffold is a computer program that integrates search results from search algorithms such as Sequest, X!tandem ,Mascot, Phenyx, OMSSA and Spectrum Mill to generate peptide identification and protein identification probabilities. Scaffold also displays an overview of the protein identifications for each search algorithm so that spectral identifications can be compared and validated by probability scores. Protein information can also be used to detect false positives and also examine the peptide and spectral evidence used for identification.

Scaffold Q+ helps in quantitation of 4-plex and 8-plex (iTRAQ) and 6-plex (TMT) biological samples.

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           New features in Scaffold

  • New Local FDR-based scoring system replaces the PeptideProphet for validating peptide identifications.
  • Modified weights for protein probability calculations are used in the ProteinProphet algorithm to more accurately model peptide assignments.
  • Protein clustering has been added to catalog protein groups sharing similar sequences.
  • New FDR filtering has been added to the standard probability filters.
  • Multi selection of proteins has been added to enable you to perform certain operations simultaneously.
  • Quantification and differential GO term filtering enable new biological questions to be considered.
  • Scaffold now supports any search engine that implements the mzIdentML HUPO standard.
  • Scaffold's mzIdentML export is now compatible with The PRIDE XML converter and Skyline, enabling the creation of spectral libraries for follow up SRM experiments.
  • The new version has also added new terms to capture different types of evidence used in protein clusters.


Scaffold has been discontinued on Citrix due to lack of use.


To run this software under Windows, connect using instruction provided in our Windows systems page.  Once logged in, navigate to

Start -> All Programs -> Scaffold4 -> Scaffold4

Scaffold viewer is available on CGL PCs.

Please send email to for gaining access to scaffold.

You then can access Scaffold program as regular PC application.

Clean Up Your Files
The C: drive on Xen (with node-locked licenses for ProteinPilot 4.5 version and Scaffold) has been getting full with input MGF files, search databases and output search results. We request that users back up and copy their .group, .sf3, MGF and other files once the searches are complete. Users can back up data to U: drive or any other location. Once you have backed up your files, remove the files from the C: drive so that there is enough space available for any new searches.

User Guide and help menu are available when you login to iron. Users are requested to save their files on their U:drive for back up. Moreover, Linux storage space can be cross-mounted on MSI Windows machines upon request (with an email to 



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