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

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

Protein Identification Tutorial

De Novo Peptide Sequencing Tutorial

Interpreting Electrospray mass Spectra


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

Contact Us

Any Questions? Contact Us.
Phone: (530) 754-9474 (we are not routeinly by the phone)
Text: (530)771-7055
Twitter DM: @ucdproteomics


Our shipping address is:
Proteomics Core Facility
Room 1414 GBSF
451 E. Health Sciences Dr.
University of California
Davis, CA 95616


Please do not use US Mail to send samples as they will likely be delayed, potentially affecting the quality of your sample.