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: an overview of the results spreadsheets generated by PAW and help with basic data interpretation. 
PAW User's Guide: an overview on how to run Comet and the PAW Pipeline.

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.

A Novel, Stable, Aqueous Glucagon Formulation Using Ferulic Acid as an Excipient

Biochemical Stabilization of Glucagon at Alkaline pH

Nascent Proteomes in Peripheral Blood Mononuclear Cells as a Novel Source for Biomarker Discovery in Human Stroke

Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani

Monoubiquitination Is Critical for Ovarian Tumor Domain-containing Ubiquitin Aldehyde Binding Protein 1 (Otub1) to Suppress UbcH5 Enzyme and Stabilize p53 Protein

Correlation of Actin Crosslinker and Capper Expression Levels with Stereocilia Growth Phases

Accurate Label-Free Protein Quantitation with High- and Low-Resolution Mass Spectrometers