Educational Links and Publications
An overview of mass spectrometry based proteomics. Includes most of the revelant information from the links found below. Written by John Klimek for first time users of PSR. Mass_Spectrometry_Based_Proteomics
This tutorial publication from the journal Proteomics works its way through several different types of mass analyzers, and describes how a mass spectrometer measures the mass/charge ratio of peptides.
Your Co-IP Experiment
This document goes over some of the sample preparation concerns unique to the Co-IP experiment. It also summarizes PSR's procedures for processing the samples, gives pointers for assessing final data from the experiment, and lists some approximate costs. Co-IP Guide.
Scaffold Viewer Users Guide
Now updated for version 3.0; an unofficial guide for installing and using the free scaffold viewer for mass spec results. Scaffold Viewer
PAW Pipeline Users Guide
The PAW Pipeline was developed by Phil Wilmarth of OHSU as an improvement over previous open source protein identification tools; the initial publication can be found here. This software package provides PSR with customizable state-of-the-art protein identification software, and has significantly increased sensitivity in larger and more complex datasets.
Proteomics: a pragmatic perspective is a recent article from Nature Biotechnology. It is a guide intended for those new to Proteomics, and is helpful for setting realistic expectations for your Proteomics experiment. It discusses issues such as how much protein you need to do an experiment, how many proteins you can reasonably expect to find, and rough ideas of how complicated it will be to get certain types of results.
Challenges for proteomics core facilities is an overview of the difficulties many labs like PSR struggle with on a day-to-day basis. It covers topics like quality control, data archiving, and funding.
The following is a selection of recent publications resulting from PSR Projects.