We have gathered from around the web pointers to quality proteomics tutorials. These are introductions to the subject aimed at scientists who are learning a new field.

Proteomics Interest Group at NIH

At this site you can hear the experts speak (turn on your PC's speakers) and see the slides that they presented to the NIH proteome research community. The archive has past seminars, symposiums, tutorials and lectures.

Hands-on Proteomics Training

A hands-on training course in proteomics lab and data analysis techniques leads you through preparing and analyzing samples. The four day course lets you learn by doing. This group also has other related courses.

Fixing Proteomics

This web site asks “Do you believe in the future of Proteomics research?” They answer “We do.” They show how they do in a number videos of clever proteomics analogies.

Mass Spectrometry

The mass spectrometry group at Vanderbilt has put together a good introduction to mass spectrometry for practitioners. It explains the different ionization methods (electrospray and MALDI) and mass spectrometer designs (ion traps, time of flight and ion cyclotron resonance). It discusses how these are combined in LC/MS and tandem mass spectrometry. Finally it discusses how this technology is applied to peptides and proteins.

Isotopes and Mass Spectrometry

Atoms of carbon have isotopes of mass 12, 13, and 14 amu. Since proteins are made of carbon (and other atoms), the mass detected by the mass spectrometer for a protein depends upon the isotopes of the protein's atoms. You can learn what this means for protein identification in this IonSource tutorial. You can also develop a feel for isotopes by using Isotopica, Isotopident or an isotope calculator to work out examples.

Electrospray Ionization

This site is an introduction to electrospray (ESI) by a company that makes electrosprays.

MS Quantization / internal standards

Suppose you know what protein is in your sample. How can you measure how much of it there is? One method of measuring the amount of the protein uses a mass spectrometer and an internal standard. This tutorial from IonSource is aimed at mass spectrometrists. If you decide to do this, you can find peptides to use as internal standards at the Peptide Resource Page.

2D Gel Electrophoresis

James Jefferies at the University of Wales provides this in-depth introduction to 2D gels. It explains how a pH gradient is formed in the first dimension by IEF and the second dimension by SDS-PAGE. It includes protocols for sample preparation and staining. There is also discussion of interfering substances and what to do about them.

HPLC - Handbook

This web site by a HPLC vender has several handbooks on HPLC available for download as pdf files. These handbooks have lots of detail on ion-exchange and reverse phase chromatography. There are a number of other HPLC web sites listed in the related links column on the left.

Antibodies tutorial

Antibodies are the gold standard in protein identification. An antibody vendor, Chemicon, has made a very nice 36 page pdf "Introduction to Antibodies". To make sense of antibody discussions, remember that what you call a protein, they call an antigen. If you want to find an antibody for a particular purpose, the Antibody Resource Page is a good place to start looking.

Protein chemist tutorials

This site has a number of tutorials on protein chemistry including purification, gels, antibodies, gels and modifications. It also has calculators for buffers and peptide characteristics.

What is Bioinformatics?

The short answer is that bioinformatics is the use of computers in molecular biology. Bioinformatics is one of the disciplines that proteomics is built upon. Bioinformatics grew up with (and is still largely focused on) genomics. This bioinformatics tutorial reflects this history in its emphasis on genomics rather than proteomics. The Bioplanet website has links to a many bioinformatics topics..