Purdue Proteomics Facility (PPF)

Overview of Services

The Purdue Proteomics Facility (PPF) provides state of the art proteomic infrastructure for the identification and characterization of proteins in a complex biological sample including label and label-free quantification, post-translational modifications (e.g., phosphorylation, glycosylation, acetylation, etc.) and protein-protein interactions. As a shared facility of the Bindley Bioscience Center (BBC) and the Purdue University Center for Cancer Research, the facility provides scientists access to various platforms for proteins and peptide separation, and highly sophisticated mass spectrometers for LC-MS and MS/MS experiments. The PPF also offers advanced scientific and bioinformatics training and consultation to the investigators, training on the use of instruments, sample preparation and LC-MS data analysis. 

If you consider sending samples to us please contact us (uaryal@purdue.edu; candolin@purdue.edu) at the early stage to schedule a meeting. This will allow us to explain the best way to prepare samples, and answer your questions, for you to answer our questions. Our mass spectrometers operated under nano flow HPLC system, and are highly sensitive. So any residual salts or detergent contamination in the sample can severely affect the performance of the mass spectrometer. For example, different detergents such as triton X, tween 20, NP-40, SDS are useful for many biological experiments, but cause serious problem even at a trace amount. So, any protein or peptide samples for mass spectrometry analysis should be absolutely free from the salt and detergents contamination. We used different methods to remove them. If your sample contains, or may contain any detergent or salt, even in a very small amount, please let us know so that we can remove them before they get into our system. 


The PPF offers following services:

Protein and Peptide Separation

  • Separation of native proteins by Size Exclusion Chromatography (SEC)
  • Offline peptide pre-fractionation prior to LC-MS/MS analyses
  • BCA assay for the measurement of protein/peptide concentration

Protein Digestion and Labeling

  • In-gel or in-solution protein digestion using different proteases (trypsin, LysC, chymotrypsin)
  • Peptide C18 clean-up
  • Phosphopeptide enrichment (using TiO2 and IMAC)
  • Peptide labeling with stable isotopes (iTRAQ, TMT, reductive methylation) for relative protein quantification
  • Fully supported workflows for the analysis of SILAC, 15N metabolic labeling samples

Mass Spectrometry

  • Identification of proteins from coomassie or silver stained gels
  • Complex proteome analysis by LC-MS/MS for identification and relative abundance profiling
  • Both labelled and label-free relative protein quantification and proteomes using high resolution and high mass accuracy LC-MS and LC-MS/MS analysis
  • Identification of phosphorylation and other post-translational modifications
  • Protein identification by MALDI TOF MS peptide mass fingerprinting
  • Data analysis using Mascot, Protein Pilot and MaxQuant


**For NON Purdue individuals: Before you register, you must be assigned a Business Partner Number and given a PUID to register/login.  

Please contact the Director and Assoicate director of the core, Uma Aryal at uaryal@purdue.edu and Venkatesh Thirumalaikumar at vpthirum@purdue.edu. An email will be sent to you with your PUID and instructions on how to get registered.


Uma Aryal, Director


Venkatesh Thirumalaikumar, Associate Director




Location and Hours of Operation

Hours Location

Monday - Friday           

9 am - 5 pm 

Bindley Bioscience Center

1203 W. State St.

West Lafayette, IN  47907

Links and Resources

Purdue Bindley Bioscience Center- Proteomics Facility


Name Role Phone Email Location
Uma Aryal

Venkatesh Thirumalaikumar
Associate Director


Service list

Search available services:
Name Description Price
Instrument set up (labor rate)

Building worklists, loading samples to vials, etc.