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Proteomics Core Facility

Neil L Kelleher, PhD

Young Ah Goo, PhD
Operations Director:


8305 Olson Pavilion
710 N. Fairbanks Ct., Chicago, IL 60611

B550 Silverman Hall
2170 Campus Drive, Evanston, IL 60208



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The mission of the Proteomics Core Facility is to provide cost-effective, state-of the-art instrumentation and analytical proteomics expertise to investigators. The proteomics Core provides a full array of services including study design, sample preparation, data generation and analysis and interpretation of results. The Proteomics Core supports investigators engaged in basic, preclinical, and clinical cancer research, including researchers examining basic mechanisms in of disease, as well as investigators seeking to identify novel targets for therapy or biomarkers that can be used for early detection, diagnosis, prognosis, or response to therapy. The Core also provides specialized services, including top-down proteomics and epiproteomics, a reflection of its distinct strengths and pioneering work in technology development.

Key Services

  • Protein identification from gels, IP and BioID samples
  • Quantitative proteomics - labeled and label-free
  • Top-down proteomics - qualitative and quantitative
  • Site-specific PTM analyses, including phosphorylation, acetylation, methylation, glycosylation, palmitoylation, and ubiquitination
  • Targeted proteomics using SRM/MRM/PRM
  • Histone Modification Panel analysis, covering all major histone marks
  • Advanced proteomics sample preparation from body fluids (blood, urine, saliva, CSF), tissue, secretome, exosome, and mitochondria


  • Thermo Q-Exactive HF
  • Thermo Orbitrap Velos
  • Thermo TSQ Quantiva
  • Thermo TSQ Quantum Ultra
  • Thermo UltiMate 3000 RSLCnano System (x4)

Highlighted Projects

Investigating mitochondrial respiration and haematopoietic stem cell function

In collaboration with Dr Chandel, a member of the LCC, the proteomics Core helped elucidating mitochondrial respiratory chain is dispensable for adult or fetal HSC proliferation, but essential for fetal HSC differentiation and maintenance of adult HSC quiescence. More information »

Epiproteomic profiling of diffuse intrinsic pontine glioma cells

In collaboration with Dr Shilatifard, a member of the LCC, the proteomics Core helped elucidating Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation. More information »

Spherical nucleic acids for cancer therapeutics

In collaboration with Dr. Mirkin, the Core contributed to this study by demonstrating that G-rich Spherical nucleic acids (SNAs) adsorb more types of proteins and more total protein from serum than do poly-T SNAs. More information »


All manuscripts and grants presenting work supported by this core should include the following acknowledgement:

Proteomics services were performed by the Northwestern Proteomics Core Facility, generously supported by NCI CCSG P30 CA060553 awarded to the Robert H Lurie Comprehensive Cancer Center and the National Resource for Translational and Developmental Proteomics supported by P41 GM108569


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