MALDI MS proteomics 2D gels electrophoresis Voyager DE-Pro
Columbia University, all rights reserved.
Quantitative Proteomics Center
Department of Biological Sciences
Applied Biosystems Voyager De Pro MALDI-TOF
This matrix-assisted laser desorption ionization time-of-flight mass spectrometer with delayed extraction is used to for identification of proteins from 2D gels using peptide mass fingerprinting (peptide mass mapping) in reflectron (high resolution mode).  In linear mode another detector is used to determine the mass of intact proteins.
IEF 2-D gels Two-dimensional gel DIGE isoelectric focusing
Electrophoresis 2D gel SDS PAGE DIGE differential gel, difference gel
Mascot Proteomics bioinformatics
Mascot Proteomics Database Server

Mascot proteomics software (Matrix Science Ltd.) running on an HP xw4400 with Intel Core2 Due Extreme x8600 processor, 4 Gb memory and 1 TB hard disk space.  This database server allows comparison between mass spectra and protein databases to facilitate the identification of proteins.
Isoelectric Focusing

Two GE Healthcare IPGphor isoelectric focusing units allow separation of proteins on the basis of charge. These units are used in the first dimension of 2D gel electrophoresis in support of the DIGE technique.   Our three units are equipped with computer logging of run progress for quality assurance.
SDS PAGE Electrophoresis

The GE Healthcare Ettan DALTsix SDS PAGE electrophoresis unit with power supply and external refrigerated circulator allows separation of proteins on the basis of size. This unit is used in the second dimension of 2D gel electrophoresis in support of the DIGE technique.   This unit is equipped with computer logging of run progress for quality assurance.
Typhoon DIGE proteomic differential gel, difference gel 2D gel
DeCyder DIGE proteomic differential gel, difference gel 2D gel
Ettan DIGE spot picker, proteomic differential gel, difference gel 2D gel
Ettan DIGE digester, proteomic differential gel, difference gel 2D gel
Typhoon Trio Laser Imager

The Typhoon Trio (GE Healthcare) is a laser scanner used for fluorescence imaging.  This system includes 3 lasers and allows imaging of three discrete images with negligible spillover for the DIGE workflow.
DyCyder 2D

This software package (GE Healthcare) is used for the analysis of relative expression of proteins based on fluorescence signals.  It uses the images produced by the Typhoon imager to detect relative differential regulation of proteins.
Ettan Spot Picker

This robotic system (GE Healthcare) picks protein spots from 2D gels and transfers them to bar-coded 96-well plates using spot coordinates generated by the DeCyder software.  
Ettan Digester

This gel plug and liquid-handling system (GE Heathcare) performs in-gel digestion of proteins in acrylamide plugs collected from 2D gels in bar-coded 96-well plates.
Synapt G2 HDMS quadrupole-time-of-flight mass spectrometer (Waters Corp.)

This quadrupole acceleration, time-of-flight mass spectrometer provides high mass accuracy for both precursor and product masses.  This innovative instrument allows mass spectra to be recorded at alternate low (precursor) and high (product) fragmentation voltages, and with the ProteinLynx Global server (see below) provides improved label-free quantitation and protein identifications. This unit is equipped with a number of innovative features including second generation high definition mass spectrometry (HDMS) capability for implementing ion-mobility separations and electron-transfer dissociation (ETD) for studying post-translational modifications.
Equipment and Software Resources
ProteinLynx Global Server biomarker proteomics PLGS MSE IdentityE
NanoAcquity UltraPerformance LC (UPLC) (Waters Corp.)

The  system is designed for nano-scale, capillary, and narrow-bore separations to attain the highest chromatographic resolution, sensitivity, and reproducibility. Direct nano-flow offers significant improvements over conventional nano-flow separations technologies. The system’s 10,000 psi operating pressure capability allows for superior high-peak capacity separations by operating longer columns packed with sub-2 m particles.
ProteinLynx Global Server (PLGS)

The PLGS software platform leverages the selectivity of exact mass data and the specificity of MS^E analysis. Combined with intelligent filtering and scoring routines, this minimizes the occurrence of false positive results.  PLGS also features Identity^E with comprehensive peptide ion accounting informatics that mines the label-free UPLC/MS^E data to identify more peptides/proteins with high sequence coverage and provides quantitation for a wide variety of samples.  Enhancements to this protein identification and quantitation software have been achieved through incorporation of support of ion mobility spectrometry (IMS) data and the parallel processing capability of our graphics processing unit (GPU) equipped computer. 
NanoAcquity UPLC for proteomic analysis
Elucidator Protein Expression Data Analysis System

Rosetta Elucidator system performs data management and analysis for label-free mass spectrometry data, for accurate peptide and protein identifications.  The Elucidator system allows our center to perform data mining and discovery of potential protein biomarkers and proteins that are differentially expressed among different tissues, cell types, affinity preparations genotypes, subcellular organelles, phenotypes, drug or other treatments.  Data mining matches accurate mass and retention time measurements for mass spectrometric features across large and complex experiments, substantially increasing usable data from each experiment.  In addition, Elucidator provides a suite of advanced statistical analysis and visualization tools for protein expression analysis.  This software is fully enabled to import both raw and processed data from PLGS (see above), fully supporting our data-independent acquisition MS^E and data-dependent acquisition workflows.
Elucidator shotgun bioinformatics proteomics software Rosetta
Synapt G2 proteomic analysis mass spec spectroscopy