Educational Links and Publications

Proteomics overview

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.

An overview of how we identify proteins using a mass spectrometer can be found here. It was written by John Klimek for first time users of PSR.

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.

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.

Phil Wilmarth's Github site

Phil Wilmarth is the primary informatics specialist in the Proteomics Shared Resource and maintains a site on GitHub for the software he has written. 

His site is geared heavily towards teaching the different methods we use here and contains explanation and insight into many different topics including: TMT data analysis, IRS Normalization, PAW Pipeline, various .fasta tools, and other relevant bioinformatics subjects. These topics are often laid out in a Jupyter Notebook with code alongside data interpretation. There's also links to several of the different scripts and programs we use in the Proteomics Shared Resource and a blog he updates. If you're looking to take your knowledge for Proteomics data analysis beyond the overviews offered here, or if you have a background in bioinformatics or programming, his site is well worth the time.

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.

OHSU researchers develop new model to study S. mutans behavior at protein level is an example of what is possible for us to do under the University Shared Resources pilot funds program.