Frequently Asked Questions

• 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

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Product Documentation

• Scaffold File Compatibility Matrix
• Elements File Compatibility Matrix
• Proteome Software Installation Guide
• Proteome Software Application System Requirements
• Proteome Software Documentation Web Site

Special Help Topics

• Running Multiple Instances of Scaffold on One Computer
• The Benjamini-Hochberg Correction
• Use of the Chromatographic System Feature in Elements
• Basic Scaffold Workflow
• Generating Scaffold and pdResult Compatible Files in One Step
• License Key Tips -- Working with Proteome Software Keys

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White Papers

• The Permutation Test
• Terminology Comparison: Legacy Scaffold and Scaffold 4
• Precursor Intensity Quantitation in Scaffold Q+
• Protein Grouping and Clustering in Scaffold
• Scaffold Q+ Normalization
• Scaffold Q+ Kernel Density Estimation

PS Product Citations

• Journal Articles Featuring Proteome Software Products
• APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data

Introductory Material

• Introduction to Metabolomics
• Introduction to Proteomics
• Question Assumptions

Presentations

• A Complete Framework for Metabolomics
• Scaffold: The New Quantify View
• Analysis of GeLCMS Data in Scaffold
• Improving Quantitation with Scaffold PTM
• X! Tandem Explained
• Ascore Explained

Conference Posters

• Proteome Software Conference Posters
• Normalizing PTM Expression by Protein-level Quantitation in Scaffold PTM
• Adjusted-median Approach to Missing Values in Label Free Quantitation

Implementation References

• X! Tandem
• Ascore
• The Prophet Algorithms

Search Engine Specific Documentation

• Configuring Mascot Distiller for Loading Quantitative Data into Scaffold Q+S

Announcements

• Sitemap File
• Proteome Software Launches New Technical Support Ticketing System