Getting Started with Scaffold perSPECtives

The following article contains a list of frequently asked question relating to getting started with Scaffold perSPECtives. For specific questions not covered in our documentation we are available by telephone Monday through Friday from 8 AM to 5 PM PST. Our toll free number is 1-800-944-6027. Additionally support can be contacted via email at

Downloading Scaffold perSPECtives

Where can I download Scaffold perSPECtives?
For a download of Scaffold perSPECtives please send correspondence to  

How do I request an evaluation key?
You can request an evaluation key from our website here. A representative from Proteome Software will be in touch with you shortly after processing the request to send a key to the e-mail address provided.

How do I install Scaffold perSPECtives?
See our Installation Guide for instructions on installing perSPECtives and find information on system requirements here. Please note that Scaffold perSPECtives is only available for 64-bit operating systems. 

Do I need to own Scaffold to use perSPECtives?
No, unlike Scaffold Q+ or Q+S, Scaffold perSPECtives operates independently of Scaffold. Scaffold perSPECtives loads data in the mzIdentML format available for export from Scaffold thus Proteome Software recommends having both programs to create a robust, seamless data processing pipeline. If you use a search engine that does not produce mzIdentML files the data can be loaded into Scaffold first then exported for analysis in perSPECtives.

Does perSPECtives have a Free Viewer? Where can I get it?
Of course! Proteome Software is committed to keeping scientific research and results accessible by offering Free Viewers of all its products. You can download the perSPECtives viewer from our website here

Is there a perSPECtivesBatch?
Scaffold perSPECtives is not available as a Batch program at this time.

Loading Data into Scaffold perSPECtives

What types of files can I load into Scaffold perSPECtives?
Scaffold perSPECtives can load mzIdentML files, versions 1.1.0 or higher. For more specific details on loading MZID files, including some exceptions, please see our perSPECtives User's Guide.

Where can I find demo data for Scaffold perSPECtives?
Scaffold perSPECtives is built with demo data pre-installed, which can be located via Help>Open Demo Files. The data is saved in the perSPECtives installation directory specified during install. 

Additional demo demo data can be found here

Do I need the MGF files when I load my MZIDs?
While MGF files are not necessary for Scaffold perSPECtives to perform its analyses, spectra will not be available for inspection without them. 

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