Proteomics Core

Proteomics Core Mission Statement


The Proteomics Core enhances research productivity by providing the equipment and trained personnel necessary for analysis of cellular protein composition, protein modification, protein quantitation and protein interaction. Proteome profiling and protein identification services utilize modern mass spectrometer based methods. The primary platform for analysis is the Thermo Finnigan LTQ Linear Ion Trap equipped with Electron Transfer Dissociation (ETD). Isolated protein, gel plug and full proteome analysis are supported. Sample preparation is achieved by robotic or manual depletion of high abundance proteins, digestion and solid phase extraction (SPE). Various sorbents including specialized sorbents such as TiO2 for isolation of phosphopeptides are available for SPE. Nanoflow HPLC from a Michrom H4 platform is utilized for most analyses with a Triversa Nanomate robot available as needed. Data analysis is achieved using Mascot, Sequest, X!Tandem and PEAKS algorithms with secondary data analysis by Scaffold. Results are distributed as hard copy on CD or by deposition on the international Tranche network. The Core enhances research productivity by providing a clear and easily accessible mechanism for protein identification and for relative quantitation of proteins based on isobaric tags. Quantitation technologies supported include cICAT, iTraq, TMT and SILAC and Multiple Reaction Monitoring (MRM). Analysis of isotopically labeled samples is achieved using the Mascot Quantitation package. MRM analysis is achieved using the TSQ Vantage with PinPoint and Skyline software for experimental design and data analysis. The protein identification component of the Proteomics Core access to technology for protein identification, proteomic profiling and biomarker identification. The protein interactions component of the Core provides instrumentation and services for detection of protein binding by Fluorescence Polarization (FP) and Surface Plasmon Resonance (SPR). The instruments in the Core produce sensitive, accurate and real time measurements of protein binding events. Thus, the protein interactions component of the Core supports investigators in asking questions about protein-protein interactions and the effects of those interactions on signaling pathways and cellular function.

Proteomic analysis contributes to our understanding of how cancers arise and is currently being developed for early cancer detection as well as therapeutic monitoring. Discovery, validation and hypothesis testing are supported using equipment that is in place and supported by trained personnel. All areas of cancer research are benefiting from proteomic technologies by developing greater understanding of the disease process. Clinically relevant proteomic analysis is expected to deliver unprecedented sensitivity in the detection of cancer and the ability to monitor the effectiveness of treatment.



The Proteomics Core is the primary and, in many instances the only, provider of services in protein mass spectrometry and protein interaction technologies at WSU. The technologies supported tend to have high equipment cost and require specialized skills for effective operation. This Core is evolving and each year since its existence, has expanded the services available and technologies supported. Continued expansion of the Core will focus on introducing additional instrumentation for mass spectrometry and expanding the software available for analysis of stable isotope labeling in quantitative proteomic experiments. Services available and technologies supported include:

  • Protein identification using nano-LC/MS/MS or MALDI ToF MS instruments
  • Protein quantitation using spectral counting or isobaric tags with data acquired on the LTQ and the Multiple Reaction Monitoring strategy using the TSQ Vantage system
  • Proteomic profiling using two-dimensional chromatographic separations or MuDPIT technologies
  • Analysis of post translational modifications using nano-LC/MS/MS with fragmentation by ETD or CID
  • Robotic protein digestion using the Genomic Solutions Investigator ProGest
  • Robotic MALDI plate spotting using the Genomic Solutions Investigator ProMS
  • Sample fractionation by liquid phase isoelectric focusing using the BD Free Flow Electrophoresis, the Invitrogen Zoom isoelectric focusing apparatus or the Cell Biosciences digital Protein Fractionator (dPF)
  • Two-dimensional chromatographic separation of cell and tissue lysates and biological fluid samples using the Beckman/Coulter PF2D. MultiView software on an off-line work station allows visualization of differences in protein composition between samples. Fractionated samples are collected in 96 well plates for further analysis.
  • Protein interaction and protease activity analysis by fluorescence polarization measurement using the Beacon 2000 fluorescence polarization system or the Tecan Polarion microplate reader
  • Peptide labeling and purification using an HPLC with UV and Fluorescence  Detectors
  • Fluorescence measurement using a QM-6 spectrofluorometer equipped for simultaneous dual emission recording and with removable dual emission polarizers all controlled by software on an accompanying work station
  • Surface Plasmon Resonance (SPR) using a Biacore 3000. Investigators performing SPR analysis must have appropriately trained personnel
  • Data Analysis using Mascot, Sequest, X!tandem and Peaks algorithms with data compilation and secondary analysis using Scaffold. Additional analysis is available through the Genomics Core.

Getting Started



Wayne State Users


All users that are not internal to Wayne State:
  • For users external to Wayne State, please register for an iLab account by clicking on the sign up link at the upper right corner of this page.  An account is required to make reservations on the core equipment calendars.
  • For general instructions on how to request services, please click on the link below.



Paul Stemmer Ph.D. | Director

Joseph Caruso Ph.D. | Co-Director

Namhee Shin M.S.




Proteomics Facility Core
Room 2105, Scott Hall of Medical Sciences
540 East Canfield
Detroit, MI, USA, 48201
Lab Phone: 313-577-6545
Fax: 313-577-6524
Email Address:

Links and Resources

  1. Proteomics Webpage
  2. DCaTS Website



Name Role Phone Email Location
Paul M. Stemmer Ph.D

Joseph A. Caruso Ph.D.

Namhee Shin M.S.
Research Assistant

Proteomics Core




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