The aim of the UTMB Mass Spectrometry Proteomics Center is to assemble state-of-the-art instrumentation and highly skilled technical staff to provide experimental capabilities required to support a broad range of molecular-level research. Mass spectrometry (MS) plays an increasingly important role in molecular-level research, and it is central to ‘omics’ research, i.e., petroleomics, proteomics, metabolomics, lipidomics, glycomics, etc. Scientists at the forefront of exciting efforts such as cancer research, energy, human health, structural biology, and drug discovery all require the ability to accurately identify, characterize and quantify important molecular species. The technological challenges that these scientists face require development of instrumentation and methods that will allow separation/isolation of exceedingly complex mixtures and identification and quantitation of specific molecules and determination of specific interactions between complexes of molecules. The long-range goal of a complete understanding of structure-function on a genomic scale requires high sample throughput, exceptional sensitivity, large dynamic range, and high reliability. The Mass Spectrometry Proteomics Center is well-equiped to facilitate these studies with a suite of LC-MS systems including the ThermoScientific Fusion Orbitrap MS, the Sciex 5600 TripleTOF, 6500 Qtrap, and 5800 MALDI TOF/TOF.

Fusion Orbitrap. Ultra-high resolution (214,000 @ 1,000Da) MS coupled to a nano-UPLC for proteomic analysis. The fusion offers three fragmentation modes; collision induced dissociation (CID), High energy collision dissociation (HCD), and electron transfer dissociation (ETD). In addition, the Fusion has MSn capabilities combined with the added functionality of electron transfer dissociation are powerful tools needed to resolve the site and type of PTM present.

5600 TripleTOF is typically used for proteomics. It is a hybrid quadrupole TOF platform, accurate mass (<3ppm), high-resolution (30,000) system than can operate by means of information-dependent acquisition (IDA) with speed (up to 50Hz) and sensitivity of a TOF MS and quantification capabilities similar to a triple quadrupole MS. When operated in a data-independent acquisition (DIA) mode, termed SWATH-MS by Sciex, the 5600 offers quantitative accuracy comparable to Selected Reaction Monitoring (SRM), and multiplexing capabilities comparable to DDA proteomics. In SWATH-MS, peptide precursors are sequentially selected in defined precursor ion mass windows for concurrent fragmentation, and the resulting fragment ion spectra are recorded in recursive cycles over the chromatography time.

6500 QTRAP system merges triple quadrapole and linear ion trap capabilities to provide the industry standard in sensitivity and selectivity. With a Dionex 3000 nanoUPLC system at the front end, the QTRAP 6500 UPLC-MS/MS system offers the ultimate sensitivity for selected reaction monitoring for quantiation, complex sample analysis (e.g. amino acids, lipids, metabolites, and peptides).

5800 MALDI TOFTOF is used for obtain masses of lipids, nucleic acids, peptides, proteins, and polymers ranging in molecular mass from 200 Da up to 100 kDa or more. For analysis by MALDI, a sample is mixed or coated with an energy-absorbing matrix and then irradiated with a laser beam (typically a Nd:Yag laser). Singly protonated (positive ionization mode) or deprotonated (negative ionization mode) molecular ions are formed and detected by a time-of-flight mass analyzer. In addition the 5800 has MS/MS capabilities, aiding in the identification of analytes. The 5800 can also be used for molecular imaging of tissues or materials.