Using Scaffold Software

A collaborative repository for user and support documentation about Proteome Software products

• Custom Digestion Enzymes Configuration in Scaffold DIA Workflows
• Commandline Arguments for Running msConvert CLI
• Connecting to your Mascot Server from Scaffold
• Transitioning from Scaffold LFQ to Scaffold DDA Label-free Quant
• JRE Licensing and Scaffold Software
• Peptide Count Columns in Scaffold DIA
• Using Scaffold Software Batch: Features and Functionality
• Running MSFragger and Sage through Scaffold
• Legacy Scaffold Elements and Scaffold perSPECtives Viewers
• Collaboration using Scaffold Software
• Determining Isolation Windows in DIA Raw Files
• DIA Proteomics Workflows: Choosing the Right Library
• Scaffold Software Comparison
• Scaffold Software User Guides
• Running Scaffold Programs on Mac Computers with macOS Catalina and Above
• Prosit-Derived Spectral Libraries for Scaffold DIA Searches
• Offline Registration for Scaffold Software
• Updating msConvert in Scaffold DIA or Scaffold Elements
• Searching FASTAs with Scaffold DIA, Resource-Intensive Process
• Isobaric Tagging (TMT, iTRAQ) and mzIdentML/MGF Files
• Accessing Wiki Pathway information from Scaffold
• Proteome Software File Extensions
• License ID Nomenclature
• Correcting Accession Number Issue with New Uniprot GO Annotation Files
• Getting Started with Scaffold: A Primer for Viewer Users
• Scaffold and Assumptions Regarding Statistical Analysis
• Use of the Chromatographic System Feature in Scaffold Elements
• X! Tandem
• Ascore
• The Prophet Algorithms