Educational Links and Publications

Proteomics Overview

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

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. PAW Results Guide.

Other Educational Links

Scripps Center for Mass Spectrometry (how a mass spec works) -

Educational Publications

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.


PSR Publications

The following is a selection of recent publications resulting from PSR Projects.

HIF1α Protein Stability Is Increased by Acetylation at Lysine 709

KHARON1 mediates flagellar targeting of a glucose transporter in Leishmania mexicana and is critical for viability of infectious intracellular amastigotes

Mechanisms of glucagon degradation at alkaline pH

Diagnostic and Therapeutic Potential of Tetanus Toxin-Derivatives in Neurological Diseases

Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

Recombinant Filaggrin Is Internalized and Processed to Correct Filaggrin Deficiency

The TonB3 System in the Human Pathogen Vibrio vulnificus Is under the Control of the Global Regulators Lrp and Cyclic AMP Receptor Protein

Distinct energy metabolism of auditory and vestibular sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity