Frequently Asked Questions

A section to quickly get FAQs about Proteome Software products

• 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
• Proteome Software Resellers
• Spectrum Count Normalization in Scaffold
• Calculations in Scaffold PTM
• Publishing Data Using Scaffold perSPECtives
• Organizing Data in Scaffold perSPECtives
• Getting Started with Scaffold perSPECtives
• Exporting and Sharing Results from Scaffold PTM
• Scaffold PTM Views and Displays
• Loading and Organizing PTM Data
• Getting Started with Scaffold PTM
• Exporting and Sharing Results Using Scaffold Q+
• Calculations in Scaffold Q+/Q+S
• Views and Displays in Scaffold Q+
• Loading and Organizing Quantitative Data in Scaffold Q+/Q+S
• Getting Started with Scaffold Q+
• Exporting and Sharing Scaffold Results
• Calculations in Scaffold
• Scaffold Views and Displays
• Using FASTA and GOA Databases in Scaffold
• Loading and Organizing Scaffold Data
• Getting Started with Scaffold
• Export Current View in Q+/Q+S to get More Decimal Places
• CID, ETD, HCD, and Other Fragmentation Modes in Scaffold