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.
This Affinity Purification Guide goes over some of the sample preparation concerns unique to the affinity purification experiments such as antibody pulldowns and click chemistry experiments. It also summarizes PSR's procedures for processing the samples, gives pointers for assessing final data from the experiment, and lists some approximate costs.
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.
The Proteomics Shared Resource maintains a educational resource on Github that covers many different topics such as the basics of LC-MS/MS analysis, and overviews of our TMT workflows. The presentations there are designed as a simple but descriptive introduction to the topics and are aimed primarily at those new to Proteomics.
Phil Wilmarth is the primary informatics specialist in the Proteomics Shared Resource and maintains his own site on GitHub for the software he has written.
His site is geared heavily towards teaching the different data analysis 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.
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.
Fundamentals: Intact protein mass spectrometry - tips and best practices is a webinar put on by Stanford University that covers many of the aspects of LC-MS analysis of whole proteins.
Protein Tags Explained provides an overview of various affinity, epitope, and fluorescent tags, and discusses their uses and capabilities.
The following is a selection of recent publications resulting from PSR Projects.
Below are links to some useful external websites that offer a variety of web-based or downloadable tools for Proteomics.
BioVenn - comparison and visualization of biological lists using area-proportional Venn diagrams
ChemCalc - molecular mass calculator
Comet - an open source tandem mass spectrometry (MS/MS) sequence database search tool
Delta Mass - database of protein post-translational modifications
Entrez - NCBI database search and retrieval system
ExPASY - proteomics tools
IonSource - mass spectrometry tools and resources
NEWT - taxonomy database browser
PepNovo - de novo sequencing of low precision MS/MS data
Proteomics Tools - from Institute of systems Biology
ProXL - Analyze, Visualize,& Share Protein Cross-linking Data
Scaffold - download free viewer to read Scaffold (.sfd) files
Skyline – open source software for analysis of SRM/MRM/PRM/DIA/SWATH data
XlinkDB - Database and tools to store, visualize and predict protein interaction topologies
MS contaminant & detergent info:
CRAPome: a contaminant repository for affinity purification mass spectrometry data