Proteome Software Home >> Proteome Software Wikispaces >> Tutorials

Welcome to Tutorials!

This section includes step-by-step tutorials and short videos

Getting Started (Scaffold basics)


Common Procedures

Scaffold Tutorials

The Scaffold Tutorial Module #1 provides steps for Loading and Organizing your data:
  1. Loading and organizing your data
  2. When should a MuDPIT analysis be selected in Scaffold?
  3. Combining search engines
  4. Running X!Tandem
  5. Selecting a scoring system
  6. Protein Grouping and Clustering
  7. Applying a FASTA database

The Scaffold Tutorial Module #2 provides steps for Viewing and Filtering your data:
  1. Setting probability thresholds
  2. Setting FDR thresholds
  3. Using the FDR browser
  4. Using bulk operations in the Samples View
  5. Adding biological information

The Scaffold Tutorial Module #3 provides examples for understanding Quantitation and Statistics:
  1. Spectral counting
  2. Quantitative values
  3. Fold change
  4. Statistical testing

Scaffold Videos

Loading Data



Loading with GO Terms



Applying and Filtering GO Terms



Quantifying GO Term Annotations



Scaffold Q+ Tutorial

The Scaffold Q+ Tutorial provides details for:
  1. Loading and organizing your samples
  2. Detecting changes over an entire experiment
  3. Statistics (with guidance for interpreting graphs in the Statistics View)
  4. Quantitative Settings (and how to determine which settings to use)
  5. Quantitative Testing (including Permutation test and the Bonferroni Correction)

Scaffold PTM User's Guide

The Scaffold PTM User's Guide provides details for:
  1. How to load data sets
  2. How to use and interpret information in each view (as well as details for each pane within a view)
  3. Tutorials that demonstrate a PTM analysis, searching and interpreting MOTIFS, and quantitation
  4. Steps and settings to create input files from Scaffold (label free data), Scaffold Q+ and Q+S (quantitative data), Mascot, and PEAKS
  5. Commands for the PTM Console (command line execution that allows batch processing)

perSPECtives Videos

Brief Introduction



Tutorial