Software 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 ProteomeSoftware.com

ProteomeSoftware.com:

Makers of Scaffold

Introduction to Proteomics

Interpreting MS/MS Results

Manual Verification of Peptide Identifications

X!Tandem Explained

Peptide Prophet Explained

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!

Molecular and Cellular Proteomics Tutorials

Molecular and Cellular Proteomics

Main Tutorial Page

De novo sequencing and homology searching (ppt)

Fourier transform mass spectrometry (ppt)

Principles of electrospray ionization (ppt)

Tutorial Presentations Presentations From Duke

Duke Proteomics Core Facility

Proteomics Tutorial Presentations

Differential Expression

Tutorial Presentations Presentations From OHSU

OHSU Proteomics Core Facility Site

OHSU Proteomics Shared Resouce

Co-IP Guide

Scaffold Guide

Challenges for proteomics core facilities

Proteomics Overview

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)

Maxquant Tutorial

Perseus Tutorial (For Maxquant Data)

MSconvert Tutorial