The Proteomics Core houses five quadrupole ion trap mass spectrometers:

  1. One ThermoFinnigan LCQ Classic
  2. Two LCQ DECA XP+
  3. Two LTQ

2010 Proteomics Equipment

Each is complete with HPLCs from Michrom (MAGIC 2002 and Paradigm MS4 HPLCs on the LCQ Classic and LCQ DECA XP+ and LTQ, respectively) or Thermo Finnigan (Surveyor Pump on LCQ DECA XP+ and LTQ) and are able to carry solvent at 200-300 nL/min into the mass spectrometers. All ion traps are equipped with custom built nanoelectrospray sources.

The Michrom Paradigm MS4 is a quaternary nano-HPLC system with 2 switching valves for operation in tandem LC (ion exchange-reverse phase) mode for analyses of complex peptide mixtures.

Separation of protein digests is achieved using fused silica capillaries (100 mm I.D. x 360 mm O.D) that are pulled (suing a Sutter Instrument Co. P-2000 Microcapillary puller) to an opening of 3-5 mm using a laser capillary puller from Sutter Instruments and packed with 7 cm of Vydac C18 material. All systems are configured for automated operation and data processing under computer control.

A proteomics training facility on the main campus is housed in Old Chemistry Building in the Chemistry Department. This training facility is equipped with one LCQ DECA XP+ and one LTQ LC-MS/MS system.


Accompanying proteomics software for protein identification using LC-MS/MS and MALDI-TOF MS data include TurboSEQUEST (the Proteomics Core has 6 licensed versions running on 6 separate web servers and has also access to a computer cluster of SEQUEST) and Protein Lynx Global Server software, respectively. We also make routine use of X!Tandem and OMSSA to search MS/MS data. Most output of data is combined within Scaffold.


  • A Micromass MALDI-LR bench top TOF instrument equipped with a reflectron, data system and Micromass Mass Lynx software for system control and data analysis.

    • This is primarily used for protein mass mapping and identification based on accurate molecular weight assignment searched and matched to peptides generated from protein databases.
  • A research grade MALDI-TOF mass spectrometer from ABI (i.e., AB Voyager DE-STR, Framingham, MA) for tissue imaging and capable also of performing post-source decay experiments

    • A dedicated Research Associate responsible for the MALDI-TOF tissue imaging initiative was hired in March 2005 as part of Dr. Lau’s recruitment to the University of Arizona.
    • A Research Specialist also assists with routine imaging (20% effort) for SWEHSC members.
  • A hybrid triple quadrupole-linear ion trap from ABI (4000 QTRAP) was awarded to Dr. Tsaprailis as PI, in a major shared instrument grant from NIH in 2005, and was installed in May of 2006. It is interfaced to an existing nano HPLC from Dionex purchased with the Voyager DE-STR MALDI-TOF mass spectrometer. The 4000 QTRAP has both a commercial ESI and nanospray source and is designed both for proteomics applications (specifically for targeted MS/MS experiments for characterizing modified peptides) and small molecule applications of higher sensitivity needs.

Other Related Equipment

  • A Michrom Paradigm MS4B protein 2D separation system.
  • The laboratory is also equipped with BioRad Protean 1D- and 2D-electrophoresis setups.
  • A Genomic Solutions UV-vis gel imager/spot picker, accompanying digester, and MALDI-target spotter are available for gel imaging capabilities and archiving. A Perkin Elmer liquid handling robot for digestions of proteins in solution and in-gel is also available.

    • These instruments provide higher-throughput preparation for MS analyses of gel and solution-based protein/peptide samples.
  • A Typhoon 9400 imager for use with DIGE (differential gel electrophoresis) technology is also available in the Proteomics Technology as part of the 2D SDS-PAGE capabilities in collaboration with the BIO5 Institute.
  • A BiaCore T100 SPR system was recently donated for molecular interaction studies.
  • New services will be available to SWEHSC soon.