Proteomics Core

Proteomics Core

Mission of the Core

The mission of the Proteomics Core is to enhance research productivity of researchers the Barbara Ann Karmanos Cancer Institute and Wayne State University School of Medicine by providing the equipment and expertise necessary for analysis of cellular protein composition and protein-protein interactions. These two objectives require different instrumentation, but they both rely on expertise in protein chemistry, separation and analysis.

The Proteomics Core is supported, in part, by NIH Center grant P30 CA022453 to the Karmanos Cancer Institute at Wayne State University.

Core Services Available

  • Protein identification using nano-LC/MS/MS instruments
  • Protein quantitation using spectral counting or isobaric tags with data acquired on the Orbitrap Fusion and Orbitrap QExactive systems 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 CID, HCD and ETD
  • Robotic sample preparation using the AssayMap Bravo robot.
  • Sample fractionation Alkaline Reversed Phase spin columns.
  • Surface Plasmon Resonance (SPR) using a Biacore 3000.  Investigators performing SPR analysis must have appropriately trained personnel
  • Biolayer Interferometry (BLI) for molecular interaction analysis using an Octet Red96.
  • Data Analysis using MaxQuant, Mascot, Sequest, X!tandem and Peaks algorithms with data compilation and secondary analysis using Scaffold.


  • Thermo Orbitrap Fusion nano-LC/MS/MS with ETD
  • Thermo Orbitrap QExactive nano-LC/MS/MS
  • Thermo Finnigan TSQ Vantage triple quadrupol nano-LC/MS/MS
  • AssayMap Bravo sample preparation robot
  • HPLC system for peptide purification, which includes UV and Fluorescence Detectors
  • Biacore 3000 for molecular interaction analysis by Surface Plasmon Resonance
  • Octet Red96 for molecular interaction analysis by Biolayer Interferometry 


Paul Stemmer, Ph.D.
Director, Proteomics Core

Joseph Caruso, Ph.D.
Co-Director, Proteomics Core

Proteomics Core Selected Publications

VanHecke GC, Yapa Abeywardana M, Huang B, Ahn YH. Isotopically Labeled
Clickable Glutathione to Quantify Protein S-Glutathionylation. Chembiochem. 2019
Sep 27. doi: 10.1002/cbic.201900528. [Epub ahead of print] PubMed PMID: 31560820.

Dubaisi S, Caruso JA, Gaedigk R, Vyhlidal CA, Smith PC, Hines RN, Kocarek TA,
Runge-Morris M. Developmental Expression of the Cytosolic Sulfotransferases in
Human Liver. Drug Metab Dispos. 2019 Jun;47(6):592-600. doi:
10.1124/dmd.119.086363. Epub 2019 Mar 18. PubMed PMID: 30885913; PubMed Central PMCID: PMC6505379.

Zhang Q, Thakur C, Shi J, Sun J, Fu Y, Stemmer P, Chen F. New discoveries of
mdig in the epigenetic regulation of cancers. Semin Cancer Biol. 2019
Aug;57:27-35. doi: 10.1016/j.semcancer.2019.06.013. Epub 2019 Jul 2. Review.
PubMed PMID: 31276784; PubMed Central PMCID: PMC6844078.

Nalawansha DA, Zhang Y, Herath K, Pflum MKH. HDAC1 Substrate Profiling Using
Proteomics-Based Substrate Trapping. ACS Chem Biol. 2018 Dec 21;13(12):3315-3324. doi: 10.1021/acschembio.8b00737. Epub 2018 Dec 10. PubMed PMID: 30421914; PubMed Central PMCID: PMC6563814.

Tan Z, Yi X, Carruthers NJ, Stemmer PM, Lubman DM. Single Amino Acid Variant
Discovery in Small Numbers of Cells. J Proteome Res. 2019 Jan 4;18(1):417-425.
doi: 10.1021/acs.jproteome.8b00694. Epub 2018 Nov 21. PubMed PMID: 30404448;
PubMed Central PMCID: PMC6465122.

Garre S, Gamage AK, Faner TR, Dedigama-Arachchige P, Pflum MKH. Identification
of Kinases and Interactors of p53 Using Kinase-Catalyzed Cross-Linking and
Immunoprecipitation. J Am Chem Soc. 2018 Nov 28;140(47):16299-16310. doi:
10.1021/jacs.8b10160. Epub 2018 Nov 13. PubMed PMID: 30339384; PubMed Central PMCID: PMC6585437.

Munkanatta Godage DNP, VanHecke GC, Samarasinghe KTG, Feng HZ, Hiske M,
Holcomb J, Yang Z, Jin JP, Chung CS, Ahn YH. SMYD2 glutathionylation contributes
to degradation of sarcomeric proteins. Nat Commun. 2018 Oct 18;9(1):4341. doi:
10.1038/s41467-018-06786-x. PubMed PMID: 30337525; PubMed Central PMCID:

Ramseyer VD, Kimler VA, Granneman JG. Vacuolar protein sorting 13C is a novel
lipid droplet protein that inhibits lipolysis in brown adipocytes. Mol Metab.
2018 Jan;7:57-70. doi: 10.1016/j.molmet.2017.10.014. Epub 2017 Nov 12. PubMed
PMID: 29175050; PubMed Central PMCID: PMC5784322.

Kim S, Carruthers N, Lee J, Chinni S, Stemmer P. Classification-based
quantitative analysis of stable isotope labeling by amino acids in cell culture
(SILAC) data. Comput Methods Programs Biomed. 2016 Dec;137:137-148. doi:
10.1016/j.cmpb.2016.09.017. Epub 2016 Sep 22. PubMed PMID: 28110720; PubMed
Central PMCID: PMC5260509.

Nakajima K, Kho DH, Yanagawa T, Harazono Y, Hogan V, Chen W, Ali-Fehmi R,
Mehra R, Raz A. Galectin-3 Cleavage Alters Bone Remodeling: Different Outcomes in
Breast and Prostate Cancer Skeletal Metastasis. Cancer Res. 2016 Mar
15;76(6):1391-402. doi: 10.1158/0008-5472.CAN-15-1793. Epub 2016 Feb 2. PubMed
PMID: 26837763; PubMed Central PMCID: PMC4863655.

Sanders MA, Madoux F, Mladenovic L, Zhang H, Ye X, Angrish M, Mottillo EP,
Caruso JA, Halvorsen G, Roush WR, Chase P, Hodder P, Granneman JG. Endogenous and Synthetic ABHD5 Ligands Regulate ABHD5-Perilipin Interactions and Lipolysis in Fat and Muscle. Cell Metab. 2015 Nov 3;22(5):851-60. doi: 10.1016/j.cmet.2015.08.023. Epub 2015 Sep 24. PubMed PMID: 26411340; PubMed
Central PMCID: PMC4862007.

Wang W, Lu Y, Stemmer PM, Zhang X, Bi Y, Yi Z, Chen F. The proteomic
investigation reveals interaction of mdig protein with the machinery of DNA
double-strand break repair. Oncotarget. 2015 Sep 29;6(29):28269-81. doi:
10.18632/oncotarget.4961. PubMed PMID: 26293673; PubMed Central PMCID:

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