Skip to main content
University of Wisconsin–Madison

Mass Spectrometry / Proteomics Facility

We are open for business! We are happy to be back. During Phase 1, we will be operating at reduced capacity. We will make every effort to keep turnaround times short as we understand there are many projects that have been waiting. We appreciate your patience and business. The UW Biotechnology Center is following University guidelines regarding COVID-19.


fruit picture

Proteomics projects may involve

1) Identification of proteins from some source

2) Measuring relative differences in protein expression

3) Finding post-translational modifications of a protein

Services we offer that will aid in protein identification include in-gel digestion from isolated gel bands/spots or in-solution digestion followed by LC/MS/MS or LC/LC/MS/MS or MALDI-TOF/TOF

We have several tools for database searching in house, such as MASCOT and Spectrum Mill, and users may use these to review their data online.

Differential protein expression projects may use the gel electrophoresis services and use PDQuest to find spots that change in intensity.  We also have expertise in using isotope labels for differential proteomics including ICAT, ITRAQ, 18O and metabolic labeling.  We have peak extractor scripts to determine ratios of peptides from the different conditions and our database tools can be modified to get protein ID using different labeling strategies.

Finding modifications to protein sequence often requires a larger amount of purified protein than a simple ID.  Intact protein measurements can indicate the extent of a modification.  Running unmodified proteins can serve as a control. Using multiple enzymatic digestions can increase coverage which increases the chance of seeing a modified peptide.  Computers are available in the facility which give users access to raw data which they may use to search for modifications.