Bindley Bioscience Center

Purdue Proteomics Facility

The Purdue Proteomics Facility (PPF) provides highly innovative methodologies and the most current technologies to generate high resolution protein profiles. As a shared facility of the Bindley Bioscience Center (BBC) and the Purdue Cancer Center, the facility enables never-before-possible analysis of post-translational modifications of the proteome. Coupled with new proteomics platforms and advanced scientific expertise, our facility provides unique opportunities to perform intact protein (‘top-down’) and peptide fragment (‘bottom-up’) analyses. Many projects in Bindley Bioscience Center employ these same technologies for biomarker discovery in health and disease – a signature research area at the BBC.

Applied BioSystems 4800

The advantages of MALDI-TOF TOF include sensitivity into the picomole range and high mass accuracy. In addition, since there is usually only a singly charged ion formed, it is a good choice for the analysis of heterogeneous samples. Furthermore, the static nature of the sample allows for multiple evaluations on a single sample.

LTQ-Orbitrap XL - Nano LC-high resolution hybrid ion trap (Thermo Orbitrap)

The Orbitrap is a sub-dalton-resolution proprietary ion trap configuration instrument that enables very high resolution analysis of peptides, post-translationally modified peptides as well as small molecule detection and quantification. The Orbitrap rivals FT-ICR mass spectrometers with an easy to use and easy to maintain setup.

NanoLC-ion trap Analysis (Agilent XCT plus)

The advantage of the ESI-ion trap is that the ESI source can generate multiple charge states allowing for increase mass range and the ion trap can perform multiple MS/MS scan with rapid scanning speed and very high sensitivity.  The XCT plus is typically coupled to the Chip Cube system for low sample volume analyses.

NanoLC-Triple quadrupole mass spec (Agilent 6410)

The Agilent 6410 triple quad provides high level sensitivity for selected ion monitoring and multiple reaction monitoring for biomarker quantification studies. The 6410 includes both ESI and photoionization capability and has an on-board Chip Cube nanoLC system.

NanoLC-TOF (Agilent MSD TOF)

The advantage of the  ESI TOF is that it utilizes both the capacity of ESI to generate multiple charge states and extend the mass range of  the spectrometer by reducing the m/z ratio of large ions and the high resolution and mass acuracy afforded the TOF instruments. This is particluarly useful when preforming PMF studies with complexed mixtures.  Furthermore, the Agilent MSD TOF can be coupled to the Chip cube.

NanoLC-TOF and NanoLC-Ion trap combined platform (Agilent MSD TOF, XCT plus ion trap and 6410 triple quadrupole)

Combing these Agilent instruments into one platform results in high resolution peak picking followed by rapid, sensitive MS/MS identification and highest sensitivity peptide monitoring with MSn capabilities on the triple quad.  The modular Chip Cube can be coupled to all three machines for identical LC conditions that enable reproducible analysis. The chip cube also allows dramatic reduction of starting material and therefore the possibility to use difficult to obtain low volume samples for deep proteome interrogation.

UPLC (Waters ACQUITY) and NanoLC-TOF/TOF Analysis  (AB QSTAR Pulsar)

This technology combines ESI ionization with the hybrid quadrupole TOF analyzer for multi charge, high resolution analysis. The system has the ability to run MS/MS for protein identification. Implementation of on-line UPLC chromatography employs novel sub-two micron particles for maximum chromatographic performance for optimized throughput, minimal carry over, and highest resolution and robustness.

Triple Quad

Proteomics Expertise

  • High throughput comparative proteomics with LCMS-MS/MS.
  • Microscale in-gel tryptic digestion.
  • MALDI MS/MS identification from in-gel digest.
  • Identification and characterization of peptide and protein modifications.
  • Amino acid analysis of peptides or proteins.
  • MS/MS of purified peptides and proteins.
  • Protein identification via database retrieval from nano LC-MS/MS in-gel tryptic digest information.
  • ESI analysis of intact proteins.
  • RP-HPLC mapping of peptides from in-gel digests with MS/MS or ESI MS/MS of spectral peaks.
  • Automated and manual computer search and analyses.
  • Bioinformatic consultation.
  • Proteomics methods development and consultation.
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Schedule an Appointment

For more information about scheduling an appointment in the Purdue Proteomics Facility,

View the Scheduling page




Purdue University
Purdue Proteomics Facility (PPF)
Bindley Bioscience Center
1203 W. State St.
West Lafayette, IN 47907-2010


Uma Aryal, PhD

Facility Director