Resources

Department of Pharmaceutical Sciences on the south campus of University at Buffalo

New York State Center of Excellence in Bioinformatics and Life Sciences (CoEBLS, the main lab) at downtown Buffalo, NY

These two sites encompass a total of 1200 sq ft of well-equipped wet-lab devoted to cell culture, biochemistry experiments (for Western-blotting, electrophoresis, ELISA, etc.), column packing, treatment of proteomic samples and preparation for quantitative analysis. Major equipment includes two ultra-centrifuges, one vacuum centrifuge, one lyophilizer, one set of solid phase purification system, one UV spectrometer, three hoods, one automatic cell counter and two incubators, as well as standard equipment for protein analysis.
There are two instrument rooms at 600 sq ft in total on the 3rd floor of CoEBLS, which house a number of state-of-the-art liquid chromatography (LC) systems and mass spectrometers:

• Thermo Orbitrap Fusion Lumos Tribrid mass spectrometer

• Thermo TSQ Altis triple quadrupole mass spectrometer

• Thermo TSQ Quantiva triple quadrupole mass spectrometer

• Thermo Dionex Ultimate 3000 nano/micro HPLC systems with WPS-3000 autosamplers

• Waters Bioseparation semi-preparation HPLC system

• Several additional nano/micro LC systems (i.e. Eksigent nano-2D, Agient 1200-series micro HPLC, Shimadzu AC20 HPLC)

Among these instruments, the key ones are the three mass spectrometers set in the lab. The Oribtrap Fusion Lumos mass spectrometer is capable of performing analysis with ulta-high mass resolution (>240,000) and mass accuracy (<3 ppm). 

The TSQ instruments, on the otherhand, offer ultra-high sensitivity and are able to significantly decrease chemical noises by using high-resolution selective reaction monitoring (SRM). Therefore, these instruments are employed for selective, sensitive and accurate quantification of specific target proteins in biological samples, e.g. antibodies biotherapeutics, antibody-drug conjugates, circulating biomarkers.

Proteome Discoverer 2.2.

TraceFinder

SIEVE 

PEAKS (Bioformatics Solutions Inc.)

Ingenuity Pathway Analysis (QIAGEN)

In-house developed R package, IonStarStat