Proteomics Services Core

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Proteomics Services Core

The Proteomics Services Core is located in the Department of Physiology and Biophysics. The main goal is to provide global proteomic profiling of samples. Please see Sample Submission Guidelines and consult with the Proteomics Core manager prior to submitting the submission form.

Global proteomics are accessed using label-free techniques with services provided on a fee-for-service basis.

Global proteomics is used for large scale identification and relative quantification of thousands of unknown proteins, typically of high or moderate abundance. This process comprises of a simple sample workflow and allows for flexibility of sample processing. This is generally referred to as discovery phase proteomics and is different from targeted proteomics. As the name implies, targeted proteomics is used for identification and quantification of specific proteins of interest. Targeted proteomics can provide relative or absolute quantification of a specific protein and is great for low abundance proteins.

Global proteomics can be accessed one of two ways, label-free or with labeling. Labeling techniques use chemical or metabolic methods to label the unknown proteins. Labeling methods generally can only be directly compared with the samples mixed and measured in the same run and require extra steps when using software for data processing. Label-free methods have higher dynamic range and greater proteome coverage than labeling methods. Processing of label-free samples is simpler and leaves less room for processing errors.

This laboratory is managed by Elizabeth Flynn

Equipment and software

  • Q-Exactive System with Ion Max Source,Proteomics-Mass-Spec.jpg
  • H-ESI II probe,
  • Cehmyx Fusion 100 syringe pump, Rheodyne 6-Port valve,
  • Easy Spray Nano Ion Source,
  • UltiMate 3000 Binary RSLC nano System
  • Proteome Discoverer 2.2


Data return

You will receive an excel file with protein identification and quantification of total ion count. The Core Manager can assist with data analysis for an additional fee.

Recommended data analysis programs

  • Proteomics provides a lot of data to evaluate, and Metaboanalyst is a free online tool available to aid in data analysis.
  • Enrichr is a good website for pathway analysis. 

Hours of Operation

  • Core hours: 8:30 a.m.-6:30 p.m. Monday-Thursday
  • Submission hours: 9 a.m.-5 p.m. Monday-Thursday. It is recommended to call or email the core before dropping off samples to ensure appropriate storage of samples.

Contact us

Elizabeth FlynnElizabeth Flynn, Laboratory Manager
Office: G567