User Guides

Our Guides for the software we use

Scaffold 4.0 QuickStart Guide

This Will Get you Started With Scaffold 4.0

Scaffold 3.0 Quickstart Guide

Our Older Guide for Scaffold 3.0. Still contains some useful info

Our First Timer Guides

New To the Facility Check here

Nice recent intro to mass spec & Proteomics on Twitter no less!

Tutorials From ProteomeSotware.com

Makers of Scaffold

Introduction to Proteomics

From ProteomeSoftware.com

Interpreting MS/MS Results

From ProteomeSoftware.com

Manual Verification of Peptide Identifications

From ProteomeSoftware.com

X!Tandem Explained

From ProteomeSoftware.com

Peptide Prophet Explained

From ProteomeSoftware.com

Scaffold Questions and Assumptions

Please read if you are new to Scaffold

Tutorials From Ion Source

Ionsource.com

Protein Identification Tutorial

De Novo Peptide Sequencing Tutorial

Interpreting Electrospray mass Spectra

Isotopes!

Other Nice Tutorials and Great Information

Tandem Mass Spectrometry from Wikipedia

The Whys and Wherefores of Quadrupole Ion Trap Mass Spectrometry

Introduction to Computational Proteomics (PLOS Computational Biology)

Introduction To Proteomics Seminar (Michael MacCoss University of Washington)

Molecular and Cellular Proteomics Tutorials

A few great tutorials from MCP

Main Tutorial Page

De novo sequencing and homology searching

Power Point Presentation

Fourier transform mass spectrometry

PowerPoint Presentation

Principles of electrospray ionization

Powerpoint Presentation

Tutorial Presentations Presentations From Duke

Duke Proteomics Core Facility

Proteomics Tutorial Presentations

Great info here!

Differential Expression

Tutorial Presentations Presentations From OHSU

OHSU Proteomics Core Facility Site  =  OHSU Proteomics Shared Resouce

Co-IP Guide

Great info here!

Scaffold Guide

This is better than ours 🙂

Challenges for proteomics core facilities

Proteomics Overview