Liquid Chromatography-Tandem Mass Spectrometer (LC-tandem MS): ThermoFinnigan’s LCQ Deca XP Plus (Xcalibur V 1.3 operating software), an ion trap tandem mass spectrometer, is a robust and sensitive instrument capable of both determining the accurate mass of peptides/proteins by electrospray ionization, and also sequencing peptides by collision induced dissociation (CID). Equipped with a nano-spray ionization source and on-line High Performance Liquid Chromatrography (MAGIC 2002 HPLC, Michrom Bioresource), our LCQ is capable of resolving and detecting 5-15 proteins in a single sample analyzed for 45 min. Data analysis is carried out by automated software applications such as TuboSEQUEST (Bioworksbrowser v 1.3) and verified manually. Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-ToF): With the availability of a large number of annotated genomes, it is increasingly easier to identify a protein based solely on the peptide mass mapping. Micromass M@LDI-LR (MassLynx V 3.5 operating software with ProteinLynx for data analysis), equipped with delayed extraction (DE) and linear/reflectron detectors, is well suited for determining peptide masses with a high degree of accuracy (100 ppm). This instrument is also equipped with a Post Acceleration Detector (PAD) capable of analyzing masses up to 200 kDa. Differential Protein Expression Analysis by 2D-PAGE: (Currently for UT/BGSU users only.) With all the associated limitations, gel based two dimentional electrophoresis is still the best method for quantitative differential protein expression analysis. The PCL houses Amersham Biocciences' (GE HealthCare) IPG-Phor (18cm strip holders) for IEF and Ettan Dalt Six (24cm x 6 gels) for 2nd dimension separation. A Personal Densitometer (PDSI) and 2D-Elite Software (Amersham) is also available for gel documentation and comparison studies. | ||||||||||||||
