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Getting Started with Scaffold perSPECtives

Downloading Scaffold perSPECtives

Loading Data in Scaffold perSPECtives

Organizing Data in perSPECtives

Using Attributes

  • What are attributes? How do I use them?
  • How do I create new attributes?
  • How do I organize the attributes of my experiment?
  • Where do I change which attributes summarize my proteins?
  • I've already set up my experiment with attributes in another program. How do I import them?

Filters and Displays

  • What is the difference between the options "Use Table Ordering" and "Use Data Dependent Ordering"?
  • Does perSPECtives have a protein filtering option?
  • Where do I set Target FDR or Number of Peptide thresholds for my data?
  • How can I select which information columns to display in a table?
  • How does perSPECtives cluster my data?
  • What does "Clear User Peptide Validation" mean?

Analyzing Data with perSPECtives

Data Visualization

  • What does the Protein Sequence Covering coloring mean?
  • Why are the identified peptides in the Protein Sequence different colors?
  • Can perSPECtives annotate my proteins with GO Terms?
  • How do I set up and apply GO Term Annotations?
  • Can I apply quantitative tests to my data?
  • How do I change which attributes block and factor my quantitative tests?

perSPECtives Heatmap

  • What am I seeing in the "Heatmap" tab?
  • How do I interpret the tree structures on the X- and Y-axes of the heatmap?
  • What is the "Selected Protein Node Correlation"?
  • What is the "Selected Attribute Node Correlation"?
  • What options do I have for coloring the Heatmap?

Preparing Data for Publication