Proteomics & Lipidomics

We provide protein and small molecule structural and functional analysis, and quantitation using state of the art technology and software applications.

 Services Available

Above:  Gusti Gartner, PhD working with the Sciex instrumentation.

  • Nano-liquid chromatography
  • Protein identification and quantitation using SWATH
  • Protein post translational modification identification
  • Lipid profiling and identification (MS/MSALL)
  • Targeted multiple reaction monitoring (MRM) for lipids


Above: Sciex 6600

  • Sciex 5600 and 6600+ TripleTOF high-resolution tandem mass spectrometers with duo- and nano-spray ion sources
  • Sciex 4000 QTRAP linear ion trap mass spectrometer
  • Dionex/ThermoFisher U_3000 RSLC and Eksigent nano- and micro-liquid chromatography systems
  • Custom chromatographic column preparation and 1D, 2D chromatographic regimes
  • Analysis software (ProteinPilot™, MarkerView™,  MultiQuant™, LipidView™, Peakview™, and SciexOS™)

This component of the Proteomics and Lipidomics Core is supported by the Center of Biomedical Research Excellence (COBRE) in Mesenchymal and Neural Regulation of Metabolic Networks and the Northern New England Clinical and Translational Research Network Programs of the National Institute of General Medical Sciences.

Application, per sample Summary of items MHIR Non-profit academic For-Profit
*Protein LCMS, Gel slice Extraction reagents, trypsin, solvents, plastics $191 $298 $382
Protein LCMS, Complex sample Extraction reagents, trypsin, solvents, plastics $106 $165 $212
Quantitative ICAT4 LCMS (per sample pair) Extraction reagents, ICAT labels, solvents, plastics $441 $688 $882
**Protein SWATH5 LCMS, Complex sample Extraction reagents, trypsin, solvents, plastics $136 $212 $272
Lipidomics6, 7
Unbiased Lipid MS/MSALL, 8, 5600 (serum) Extractions, solvents, glassware, etc. $46 $72 $92
Unbiased Lipid MS/MSALL, 5600 (tissue) Extractions, solvents, glassware, etc. $48 $75 $96
Targeted precursor ion scan, 4000QTRAP (serum) Extractions, solvents, glassware, etc. $51 $80 $102
Targeted MRM, 4000QTRAP (tissue) Extractions, solvents, glassware, etc. $53 $83 $106

*A $40/hr charge is applied per project for bioinformatics data analysis. **Pricing is for mouse or human samples: An additional sample charge may apply if a new SWATH spectra database is needed 9.


1. Romero D, O’Neill C, Terzic A, Contois L, Young K, Conley BA, Bergan RC, Brooks PC, Vary CPH. Endoglin regulates cancer-stromal cell interactions in prostate tumors. Cancer Res. 2011;71:3482–3493

2. Young K, Conley B, Romero D, Tweedie E, O’Neill C, Pinz I, Brogan L, Lindner V, Liaw L, Vary CP. Bmp9 regulates endoglin-dependent chemokine responses in endothelial cells. Blood. 2012;120:4263-4273

3. Young K, Tweedie E, Conley B, Ames J, FitzSimons M, Brooks P, Liaw L, Vary CP. Bmp9 crosstalk with the hippo pathway regulates endothelial cell matricellular and chemokine responses. PLoS One. 2015;10:e0122892

4. Guaragna A, Amoresano A, Pinto V, Monti G, Mastrobuoni G, Marino G, Palumbo G. Synthesis and proteomic activity evaluation of a new isotope-coded affinity tagging (icat) reagent. Bioconjug Chem. 2008;19:1095-1104

5. Huang Q, Yang L, Luo J, Guo L, Wang Z, Yang X, Jin W, Fang Y, Ye J, Shan B, Zhang Y. Swath enables precise label-free quantification on proteome scale. Proteomics. 2015;15:1215-1223

6. Stohn JP, Wang Q, Siviski ME, Kennedy K, Jin YR, Kacer D, DeMambro V, Liaw L, Vary CP, Rosen CJ, Prudovsky I, Lindner V. Cthrc1 controls adipose tissue formation, body composition, and physical activity. Obesity (Silver Spring). 2015;23:1633-1642

7. Liaw L, Prudovsky I, Koza RA, Anunciado-Koza RV, Siviski ME, Lindner V, Friesel RE, Rosen CJ, Baker PR, Simons B, Vary CP. Lipid profiling of in vitro cell models of adipogenic differentiation: Relationships with mouse adipose tissues. J Cell Biochem. 2016

8. Simons B, Kauhanen D, Sylvanne T, Tarasov K, Duchoslav E, Ekroos K. Shotgun lipidomics by sequential precursor ion fragmentation on a hybrid quadrupole time-of-flight mass spectrometer. Metabolites. 2012;2:195-213

9. Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of swath ms data. Nat Protoc. 2015;10:426-441

Contact Us

Director: Calvin Vary, PhD

Manager: Gusti Gartner, PhD

Service Request

Service forms must be filled out completely with as much detailed information as possible.  The completed form must include the signature and account number of the Principle Investigator of the lab requesting services.  Completed forms should be submitted to Gusti Gartner (Vary Lab).

For Mass spectrometry servcies: complete Service Request Form

  • Protein identification-{Complex mixtures, gel slice, immunoprecipitation}
  • Protein Multiple reaction monitoring (MRM) assay development
  • SWATH Protein analysis
  • MSMSALL Lipidomic profiling (5600 TTof)
  • Targeted Precursor ion lipid profiling (4000QTRAP)
  • Other services include small molecula assay development, protein post-translational modification etc.-Please contact for more info.
Email completed form(s) to
Phone: (207) 396-8269/ Fax: (207) 396-8179