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Proteomics and Systems Biology Core (Penn)

Director: Blair, Ian A., Ph.D.


The Proteomics Core Facility in the Penn Genomics Institute is a service and collaborative research resource that balances applied proteomics research with the development of new and improved methods for protein identification, characterization, and quantification. The facility encourages collaborations that apply the tools of proteomics to cutting edge biomedical research.

The Proteomics Core Facility is a center not only for services but also for basic and collaborative research and development of two-dimensional gel electrophoretic - and mass spectrometric-based techniques. Prospective users are encouraged to make their inquiries either by e-mail (ian@spirit.gcrc.upenn.edu), or stop by our facility on the eighth floor of BRB II/III.



    Member: Yuan, Chao-Xing, Ph.D.
    Role: Adjunct Assistant Professor, Department of Pharmacology, Technical Director, Proteomics and Systems Biology Core



  • Applied Biosystems Q-Star Pulsar hybrid mass spectrometer with Eksigent NanoLC system ( Liquid chromatography mass spectrometry platform )

    "Developed specifically for nanospray mass spectrometry (MS), Eksigent NanoLC systems provide speed, sensitivity, resolution and reliability for your research."

    This is a hybrid quadrupole time-of-flight mass spectrometer capable of peptide identification and location of post-translational modifications.

  • Ettan DALT II electrophoresis unit ( 2D gel electrophoresis apparatus )

  • Ettan IPGphor 3 isoelectric focusing unit ( Isoelectric focusing device )

    "Ettan IPGphor 3 IEF system is a fully integrated isoelectric focusing system optimized to deliver speed and reliability in the first dimension of 2-D electrophoresis."

  • Ettan spot picker ( 2D gel spot exciser )

    "Ettan Spot Picker is designed to reproducibly spot protein samples and matrix on multiple MALDI MS targets for subsequent analysis by mass spectrometry. Samples are presented to the Ettan Spotter in 96-well microplates. The instrument acts directly on Ettan Digester output files, which provides automated sample tracking from spot picking through to digestion and completion of spotting. The easy-to-use software allows the selection of default or customizable spotting methods. Ettan Spotter uses a single needle for spotting, which is overlaid with a hydrophobic coating for eliminating cross-contamination between samples as well as any carryover of liquid. The needle is automatically washed after spotting a sample.

    There is no need for a desalting step prior to spotting since salt levels are controlled during the digestion methods used in Ettan Digester. The software enables the sample to be spotted twice on the MALDI target in order to allow sample concentration.

    Up to 384 samples can be spotted in automated mode. Throughput is determined by the number of microplates used (up to four microplates can be used) with digested material that can be fitted onto the platform."

  • Thermo Scientific TSQ Vantage triple quadrupole mass spectrometer with Eksigent NanoLC 2D system ( Liquid chromatography mass spectrometry platform )

  • Typhoon 9410 gel imager ( Gel imaging system )

    There are three scanning options for Typhoon instruments:
    • Storage phosphor screen scanning
    • Fluorescent scanning
    • Chemiluminescent scanning

    The fluorescent scanning mode has four excitation wavelengths 532, 633, 457 and 488 nm.



  • DeCyder 2-D Differential Analysis software ( Software )

    "DeCyder 2-D Differential Analysis Software (DeCyder 2D) v7.2 is specifically designed for 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE) analysis and is a key element in the Ettan™ DIGE system. Unlike other 2-D electrophoresis methods, DIGE allows the option of reference to an internal standard for each spot, effectively eliminating gel-to-gel variation and delivering highly accurate, reproducible, and dependable quantitation. DeCyder 2D applies a gel comparison method that introduces zero statistical error, offering reliable data and analysis for 2-D DIGE experiments."

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Last updated: 2016-02-01T10:14:50.345-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016