Frequently Asked Questions

A section to quickly get FAQs about Proteome Software products

• How to Completely Remove Scaffold from Your System
• Recommended FDR Settings for Loading Spectrum Mill Data into Scaffold
• Reference Libraries Used in Scaffold DIA
• DIA Proteomic Searches and FASTA File Size (Number of Entries)
• Processing Vendor Raw Data with ProteoWizard
• Scaffold Products and High Resolution Displays
• Changing Temp Space For Each Scaffold Batch Run
• Scaffold "Versioning Problem" Error Message
• Scaffold PTM Views and Displays
• Views and Displays in Scaffold Q+
• Using FASTA and GOA Databases in Scaffold
• Export Current View in Q+/Q+S to get More Decimal Places
• CID, ETD, HCD, and Other Fragmentation Modes in Scaffold
• Waters PLGS IdentityE Data Support in Scaffold
• FDR, Decoy Hits, and Forward/Decoy FASTAs in Scaffold
• Using MudPIT in Scaffold Analyses
• Parentheses in Scaffold Excel Exports
• Getting Started with Gene Ontology Annotations in Scaffold
• How do I add organism-specific GOA databases to Scaffold
• What do the Quantitative Value Tags Mean: Value Missing, No Values, Reference Missing, or No Data
• Where can I find general, in-product help