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Midwest Proteome Center (Mass Spectrometry)

This facility serves the ongoing research endeavors on campus and the scientific community as well as drug industry by providing state-of-the-art modern technologies. These include NIH – funded instrumentation and professional level of service for analysis of proteins, drugs, and metabolites. The facility has a strong commitment to be at the leading edge of current and developing approaches and provides consultation on their applications.

Biological Applications 

The Midwest Proteome Center has technological capabilities and expertise for separation and identification of proteins including sequencing, post-translational modifications, and interactions, and quantitation of proteins with  decades of expertise using  state-of-the-art instrumentation at reasonable cost.

We specialize in the use of complex biological samples from blood, brain and CSF for biomarker studies.

Bioinformatics support is available with top software tools (Spectronaut, PD, PEAKS, ProSight, Skyline, etc.) with public & proprietary databases.  We also have computational chemistry packages for structural biology in conjunction with our Crystallography Facility.

Industry Applications 

The Midwest Proteome Center has expert capabilities for identification of proteins including sequencing, post-translational modifications, and interactions. Additionally, quantitation of proteins and metabolites are facilitated with our proteomics and metabolomics expertise. We also  focus at the nexus  of biomarker and drug discovery initiatives and validation for industry through target identification, quantitation, and validation to study mechanisms, dynamic efficacy, and toxicity from biological fluids. We welcome inquiries from the Pharmaceutical industry seeking information on how we may assist them in furthering their R&D and QC goals.

Intake Form

All users must fill out the intake form, and submit it to Dr. Charlie Yang (BSB L.132-139 P: 847-578-8310)

Instruments & Capabilities 

Thermo Orbitrap Elite coupled with  an Ultimate 3000 RSLC-NANO LC System

  • Work horse mass spectrometer with superior scanning speed and accuracy.
  • Provide a wide range of protein, peptide and small molecule analysis
  • Identify and characterize post-translational modifications of proteins. 

GE Typhoon FLA 7000 PhosphorImager

  • Highly sensitive laser scanner for radioactive & fluorescent imaging.
  • Applications for DNA, RNA, and proteins.
  • ImageQuant image analysis.

Thermo Orbitrap Exploris 240 mass spectrometer

  • LC-MS/MS for proteomics and metabolomics.
  • High sensitivity/accuracy for quantitation with DIA + DDA modes.
  • Increasing determination of linear dynamic range for proteins, peptides, and drug metabolites.

908 Devices ZipChip System

  • Robust tool for separation of proteins, peptides, antibody drug conjugates, and other biological molecules.
  • Fast analysis of molecules coupled with mass spectrometer.
  • Tolerant of sample matrix.

ProteinChip series 4000 mass spectrometer (SELDI)

  • Predict drug response and biomarker discovery
  • Provide a rapid detection of protein expression profile
  • Fast and simple preparation of samples

GE Health Ettan Spot Picker

  • Excellent tool for picking spots from 2D gels.
  • Batch process multiple analyses for high throughput.
  • Extremely stable and automatically transfers to a 96-well plate.



Internal Rate

External Rate

Typhoon FLA7000 Scanner

$38/first half hour, then $17/half hr

$61/first half hour, then $28/half hr




Orbitrap Elite system ESI MSn



Orbitrap Exploris 240 ESI MSn with ZipChip or RSLCnano system



  • No initial consultation fees.
  • Onsite help always available.

Sample Preparation Tips:

1. Identification of Proteins

  • Tip 1: Gel-based samples should be destained before sending to the facility. If the low abundant proteins can not be visualized with Coomassie blue staining, silver staining can be helpful for the sensitivity and accepted by our facility.
  • Tip 2: Solution-based samples should avoid additives and detergents, such as glycerol, NaN3 (azide), DMSO, SDS, phosphate, 1M urea, 1M guanidine, sucrose, TritonX-100 (<0.01%). Discuss with the facility manager use of specific detergent.
  • Tip 3: To avoid the contaminants, such as Keratin (very common), wearing gloves and working in the lab hood will always be necessary.

2. Quantitation of Proteins

  • Tip 1: Depletion of highly abundant proteins, such as Albumin, IgG, etc., will be necessary before sending samples to the facility if derived from a human source or tissue culture.
  • Tip 2: Sample concentration for quantitation should be at least 1 ug/uL, 10uL is the minimum volume required. 

3. Analysis of Post-Translational Modifications (PTMs)

  • Tip 1: The chemical stability of the PTMs is crucial for efficient detection, avoiding the additives that could lead to extra reactions will be necessary. Discussing with the facility manager for your specific additives.
  • Tip 2: We don’t pursue PTM mapping by direct LC-MS/MS of crude cell lysate. This limits accuracy of detection with the presence of abundant unmodified peptides, inadequate peptide separation by LC, and potential ion-suppression in MS. The enrichment of PTMs will be necessary before LC-MS/MS analysis. Discussing with the facility manager for the analysis of specific PTMs.


Please acknowledge these grants in publications: NIH NCRR S10 OD010662 and HRSA C76 HF03610-01-00