Publishing Data Using Scaffold perSPECtives

The following article contains a list of frequently asked question relating to publishing 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

Preparing and Publishing Results

What information is contained in the Publish view?
The publish view in perSPECtives contains information regarding the main parameters characterizing the current experiment. Values colored in golden yellow are not specified and require more input from the user. Information about the last time the parameters were updated is hidden. The user can display the information by selecting the hidden columns in the Column Control button in the top right corner of the Publish view table. 

What exports are available in perSPECtives?
Scaffold perSPECtives exports four different Excel reports for sharing data and publication:

  • Samples report: saves information contained in the Samples view along with details of the experimental parameters
  • Peptide report: saves information regarding peptides found in each proteins including sequence, variable and fixed modifications, mass, and start and stop position along with details of experimental parameters
  • Heatmap report: saves information used to generate the Heatmap along with details of the experimental parameters
  • Publish report: saves information contained in perSPECtives' Publish view

What information is contained in the Attributes file export?
The attributes file contains the meta-data associated with individual MS samples loaded into the current Scaffold perSPECtives experiment. This file can then be imported into other programs or other perSPECtives experiments.

What information is contained in the SQL query export?
Scaffold perSPECtives SFDB files are SQL based and therefore custom SQL queries can be written in order to access data not displayed in the user interface. Users can access the SQL interface using The Run SQL Query for Export option from the Export menu or from the SQL Export tab in the Publish view.

Can I export graphics from a perSPECtives experiment?
Yes when the mousing over an image the right-click menu allows users to save images as files for publication or collaboration. 

Sharing perSPECtives Files

Does Scaffold perSPECtives have a free viewer?
As with all other Proteome Software products perSPECtives comes with a free viewer to make collaboration with colleagues easier. Simply have your collaborators download the free viewer here, you can then send them a copy of the perSPECtives SFDB file for viewing. While the viewer does not have all the functionality that the full program has it allows for viewing results using the program's interface which is preferable to sending multiple Excel spreadsheets. 

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