Frequently Asked Questions

A section to quickly get FAQs about Proteome Software products

• Is Scaffold Software compatible with M1 and M2 Apple computers?
• Installing Scaffold Software when installations are blocked by your operating system
• Scaffold t-test
• Searching with MSFragger and X! Tandem in Scaffold 5
• Why use reviewed FASTA entries for generating Prosit libraries
• Free Scaffold Viewer
• Running More Than One Copy of Scaffold
• Windows Smart Screen and Installing Scaffold
• Scaffold DIA Error: Percolator Exited with Non-zero Status
• How to Completely Remove Scaffold from Your System
• Upgrading Scaffold, Workstation Hardware, or your Operating System
• Scaffold Scoring Models and Filtered Data
• Recommended FDR Settings for Loading Spectrum Mill Data into Scaffold
• UniProt FASTA References
• Reference Libraries Used in Scaffold DIA
• Moving Scaffold Software from One Computer to Another
• DIA Proteomic Searches and FASTA File Size (Number of Entries)
• Processing Vendor Raw Data with ProteoWizard
• Scaffold DIA FASTA Searches Do Not Support Multiple Variable Modifications
• Scaffold DIA Search Performance Benchmark
• Scaffold Products and High Resolution Displays
• Changing Temp Space For Each Scaffold Instance
• Gene Ontology: Custom Annotations in Scaffold
• Scaffold "Versioning Problem" Error Message
• Running Multiple Instances of Scaffold on One Computer
• Spectrum Count Normalization in Scaffold
• The Benjamini-Hochberg Correction
• The Permutation Test
• Scaffold PTM Views and Displays
• Views and Displays in Scaffold Q+S