Frequently Asked Questions

A section to quickly get FAQs about Proteome Software products

• 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
• Using FASTA and GOA Databases in Scaffold
• Protein Grouping and Clustering in Scaffold
• Export Current View in Q+S to get More Decimal Places
• CID, ETD, HCD, and Other Fragmentation Modes in Scaffold
• Waters PLGS IdentityE Data Support in Scaffold
• License Key Tips: Working with Proteome Software Keys
• Normalization used in Scaffold Software
• Scaffold Q+S Kernel Density Estimation
• 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
• Location of Scaffold Software Parameter and License Key Files
• 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