Proteomics and Mass Spectrometry Program (PMSP)

Provides next-generation mass spectrometry and data analysis tools to quantify proteins in biological fluids and tissues.

The ICTS Proteomics and Mass Spectrometry Program (PMSP) offers next generation mass spectrometry and data analysis tools for global and targeted protein quantification in biological fluids and tissues. Consultation on experimental design, selection of analytical platforms and sample preparation are provided. The program offers integrated proteomic workflows for discovery and verification of protein targets in biological fluids and tissues. Development of high-precision, quantitative assays is available using antibody (high-sensitivity ELISA) or antibody independent methods (stable isotope dilution MS). Phosphoproteomics of tissue samples and quantitative analysis of specific protein phosphorylation sites has recently been added as a service.

Services & Resources
  • Procurement and sample preparation methods for proteomic and phosphoproteomic analyses
  • Access to software tools for global (fold change) and targeted (pg/mg total protein) quantitative proteomics.
  • Customized database construction for high-specificity analysis of post-translational modifications.
  • Quantitative isotope-dilution mass spectrometric measurements of targeted peptides.
  • Development of quantitative ELISA assays for candidate protein biomarkers using the high-sensitivity (fg/mL) Singulex platform.
  • Centralized data structure for access, storage, backup and retrieval of raw and processed MS data.
  • Standard and customized reports for the interpretation and publication of proteomic data sets.
  • Pathways and network analysis tools that integrate RNA and protein expression data.

See pictures and descriptions of our barocycler (pdf) setup and operation for sequential endoprotease digestion of tumor tissue.

ICTS Metabolomics Core

The Washington University Metabolomics Facility is a CLIA (Clinical Laboratory Improvement Amendment) certified laboratory providing the following services.

  • Targeted metabolomics analysis
  • Pharmacokinetics (PK) and Pharmacodynamics (PD) studies
  • Bioanalytical Method Development and Validation
  • Pre-clinical and Clinical Sample Analysis

For more information about the services provided by this core, see the website.

Facilities & Other Resources

For a description of the PMSP and other ICTS resources, see the Tools and Resources page.


River Blindness
PMSP will analyze fluid samples from healthy individuals, people infected with the parasite responsible for river blindness, and individuals with infections caused by other parasites to identify exclusive markers in support of a $2 million award to Gary Weil, MD from the Bill and Melinda Gates Foundation.

PMSP-affiliated Publications

  • Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O’Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK. DNMT3A Mutations in Patients with Acute Myeloid Leukemia. N Engl J Med 2010: 363, 2424-2433. PMID: 21067377, PMCID: PMC3201818
  • Perrin RJ, Craig-Schapiro R, Malone JP, Shah AR, Gilmore P, Davis AE, Roe CM, Peskind ER, Li G, Galasko DR, Clark CM, Quinn JF, Kaye JA, Morris JC, Holtzman DM, Townsend RR, Fagan AM. Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer’s disease. PLoS One 2011: 6(1): e16032. PMID 21264269, PMCID: PMC3020224
  • Chen ZW, Fuchs K, Sieghart W, Townsend RR, Evers AS. Deep amino acid sequencing of native brain GABAA receptors using high-resolution mass spectrometry. Mol Cell Proteomics 2012: 11(1): M111.011445. PMID: 22338125, PMCID: PMC3270104
  • Morales DM, Townsend RR, Malone JP, Ewersmann CA, Macy EM, Inder TE, Limbrick DD Jr.  Alterations in protein regulators of neurodevelopment in the cerebrospinal fluid of infants with posthemorrhagic hydrocephalus of prematurity. Mol Cell Proteomics 2012: 11(6): M111.011973. PMID: 22186713
  • Tiriveedhi V, Conzen KD, Liaw-Conlin J, Upadhya G, Malone JP, Townsend RR, Kerns R, Jia J, Csontos K, Ramachandran S, Mohanakumar T, Anderson CD Chapman WC, The role of molecular chaperonins in warm ischemia and reperfusion injury in the steatotic liver: A proteomics study. BMC Biochem 2012: 13, 17. PMID: 22962947
  • Marionneau C, Lichti CF, Lindenbaum P, Charpentier F, Nerbonne JM, Townsend RR, Mérot J, Mass spectrometry-based identification of native cardiac Nav1.5 channel α subunit phosphorylation sites. J Proteome Res 2012. PMID: 23092124
  • Klco JM, Spencer DH, Lamprecht TL, Wylie T, Magrini VJ, Hundal J, Walker J, Varghese N, Gilmore P, Lichti CF, Meyer MR, Townsend RR, Wilson RK, Mardis ER and Ley TJ, Genomic impact of transient low-dose decitabine treatment on primary AML cells. Blood 2012, in press.
  • Andley UP, Malone JP, Hamilton PD, Ravi N, Townsend RR. Comparative proteomic analysis identifies age-dependent increases in the abundance of specific proteins after deletion of the small heat shock proteins αA- and αB-crystallin. Biochemistry. 2013: 52(17):2933-48. PMCID: PMC3690595
  • Yip GM, Chen ZW, Edge CJ, Smith EH, Dickinson R, Hohenester E, Townsend RR, Fuchs K, Sieghart W, Evers AS, Franks NP. A propofol binding site on mammalian GABAA receptors identified by photolabeling. Nat Chem Biol. 2013; 9(11):715-20. PMCID: PMC3951778
  • Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; NCI CPTAC. Proteogenomic characterization of human colon and rectal cancer. Nature. 2014: 513(7518):382-7. PMCID: PMC4249766
  • Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H; Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG. CPTAC Assay Portal: a repository of targeted proteomic assays. Nat Methods. 2014 Jul;11(7):703-4. PMCID: PMC4113142
  • McNulty SN, Rosa BA, Fischer PU, Rumsey JM, Erdmann-Gilmore P, Curtis KC, Specht S, Townsend RR, Weil GJ, Mitreva M. An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis. Mol Cell Proteomics. 2015 Dec;14(12):3224-33. doi: 10.1074/mcp.M115.051953. Epub 2015 Oct 15. PMID: 26472727 [PubMed – in process]
  • Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016 May 25;534(7605):55-62. doi: 10.1038/nature18003. PMID: 27251275 [PubMed – indexed for MEDLINE]
  • Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. 2016 Jun 28. pii: S0092-8674(16)30673-0. doi: 10.1016/j.cell.2016.05.069. [Epub ahead of print]. PMID: 27372738 [PubMed – as supplied by publisher]
Request a Service

Email or call 314-362-7709 for consultation or inquiries.

Service available to:
All entities, including for-profit organizations, with priority given to members of the ICTS and centers listed in the “Affiliations” below.

Service Fees (pdf)


Visit our Proteomics Core Laboratory website for more detailed information.


Reid Townsend, MD, PhD, Co-Director

Henry Rohrs, PhD, Associate Director