Proteomics & Mass Spec: Instrumentation

The Proteomics/mass spectrometry facility is well equipped for analysis of ‘omics molecules. In addition to support our scientific investigators, we also provide comprehensive bioanalytical services for small molecules and/or protein-based drugs to biotechnology and pharmaceutical companies at every stage of drug development. A broad range of capabilities allow us to apply the best solution to your problem.

ABSCIEX 6500 QTRAP mass spectrometer
The QTRAP 6500 mass spectrometer is configured with ESI and APCI Turbo V source, nanospray III source, linear ion trap with mass range of m/z 5 -2000, Shimadzu Nexera LC-30AD UHPLC pumps and Nexera SIL-30 AC autosampler for high throughput. The instrument, sample introduction system, and the data acquisition as well as data processing are controlled through an Analyst 1.62 software and/or LC solutions v5.51 by a contact closure. The database search function is through a Proteinpilot version 4.5 or Mascot 2.3 algorithm (Matrix Science). Software Skyline from the MacCoss Lab at the University of Washington is used for monitoring proteins and peptides in biological samples for applications such as target verification and validation, PTM characterization, and other targeted quantitative proteomics applications. The unique MIDASTM workflow enables high throughput validation and quantitation of bio-molecule targets discovered through genomic or proteomic experiments. LightSight version 2.3 software is available for building and optimization of metabolite MRM quantitative assays on the QTRAP system. It also enables the coupling of sensitive triple quadrupole mode survey scans, such as neutral loss or precursor ion, with highly sensitive full-scan MS/MS data for structural characterization, which makes metabolite identification and quantitation more efficient than ever before. MultiQuant Software version 2.1 provides a comprehensive package for quantitation of small molecule compounds, large molecule biomarkers and biopharmaceuticals on the QTRAP system. It supports the analysis of large numbers of samples, peptides and MRM transitions in addition to the MIDAS Workflow, Scheduled MRM Algorithm assays, and labeled and unlabeled workflows for relative and absolute quantitation.

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
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.



Contact Information

Core Director

Qishan Lin, Ph.D.

(518) 591-7214


Jinghua Zhu, M.S.

(518) 591-7220