Instrumentation
The Proteomics Core Facility is well equipped for detailed studies on protein separation and
characterization, as well as related services including high-resolution 2D gel electrophoresis,
sequence analysis of protein and peptides at maximum sensitivity, in-situ proteolysis of proteins
in 1D or 2D gels, and peptide mapping. Major instrumentation at this core facility includes the following:
AppliedBiosystems QSTAR XL mass spectrometer
The QSTAR XL mass spectrometer was purchased through the NIH shared instrumental grant and brought in line in September 2005. It is operated with electrospray, photospray, oMALDI™ 2 source with a mass range of m/z 5- 40,000 and mass resolution of 10,000(FWHM). The QSTAR posses parent ion scanning function, which is very usefully for the study of post-translational modification including phosphorylation and glycosylation as well as metabolite id. Configured with a Dionex Ultimate plus dual gradient HPLC system, this instrument is superior for cICAT, iTRAQ, and SILAC labeling analysis. 
Micromass Q-TOF 2 mass spectrometer
The Q-TOF 2 was purchased through The Research Foundation of SUNY in 2002. It is operated with nanospray ionization, a low flow electrospray that offers superior sensitivity while consuming small sample volume. On-line capillary HPLC-MS(/MS) is used for complex or dirty samples. This is ideal for samples containing a mixture of peptide digest fragments originating from proteins excised from 2D-gels. The accurate mass capability as well as high resolution of this MS/MS instrument allows for peptide de novo sequencing. Configured with an on-line Waters CapLC system as well as a Z-nano-electrospray source, this system offers accurate, rapid and sensitive peptide and protein identification from both gels and mixtures in solution. 
Autoflex® MALDI-TOF mass spectrometer (Bruker Daltonics)
The Autoflex was installed in May 2004. It meets the needs of research scientists in drug
discovery and development and other areas of life science research, like proteomics and
genomics. It meets the challenges of the post-genomic era: recognizing genomic variability,
reading proteomes of countless cell types and variability, and exploring functions of millions
of proteins. The Autoflex is the first MALDI-TOF system designed for high sample throughput
and ultra-fast, automated analyses: automated processing of targets in MTP format. The
robot stores and operates 20 MALDI targets, feeding the Autoflex continuously. More than
30,000 samples are processed without operator intervention.
High-resolution 2D gel electrophoresis system
Two-dimensional gel electrophoresis remains the highest-resolution analytical method for proteins, working through separation
of proteins using two disparate physical properties: isoelectric point (pI) and relative molecular
weight (MW). We have three assemblies available for the 2D gel system including an Ettan
IPGphor IEF system and an Ettan DALTsix Separation Unit from Amersham Biosciences, Inc.,
a ProXPRESS proteomic imaging system from PerkinElmer Life Sciences, Inc., and Progenesis
imaging analysis software from Nonlinear Dynamics, Inc. 2-DE is a challenging, time
consuming methodology. Researchers will find great saving, in the time and money, by using
the expertise at the CFG.
Imaging system (PerkinElmer ProXPRESS and Nonlinear Dynamics Progenesis)
The ProXPRESS Proteomic imaging system provides unparalleled flexibility, enabling the use
of all dyes in the UV and VIS spectrum range with its CCD-based detection and multi-wavelength
emission and excitation capabilities. ProXPRESS is optimized for sensitive and high-resolution
detection and quantitation of low abundant protein.
With the Progenesis bioinformatic tool from Nonlinear Dynamics, 2D gel image analysis
is automatic and robust with minimal user intervention.
ÄKTA Explorer FPLC system (Amersham Biosciences)
ÄKTA™ explorer system is designed for fast development and optimization of protein
purification, using one working platform for all techniques and samples. Pre-programmed
method templates and optimized system configurations, allow rapid media screening, method
scouting, method optimization and scale up experiments. Standard system configurations are
available to suit most purification needs, but are easily modified if required. This system is
suitable for down-stream high-throughput sample fractionation.
Agilent 1100 HPLC system
The Agilent 1100 HPLC system has been developed as a scalable, open platform with the
flexibility to adapt to novel technologies and evolving user needs. The platform can be
configured for a variety of applications, from cutting-edge proteomics research to QA/QC
work and from measuring attomoles of peptides to purifying grams of sample. We use this
system to prepare samples for downstream mass spectrometry analysis.