Bio-Organic Biomedical Mass Spectrometry Resource

Bio-Organic Biomedical Mass Spectrometry Resource

Research Emphasis

The resource employs mass spectrometric techniques to develop improved strategies and methodologies for characterizing protein expression, regulation and protein-protein interactions, including the use of quantitative strategies that allow study of dynamics, for example in disease states. The resource has a strong emphasis in the analysis of post-translational modifications (PTMs) including O-GlcNAcylation, phosphorylation, methylation, acetylation and ubiquitination. Methodologies include a range of chromatographic strategies to separate or enrich specific post-translational modifications from complex mixtures, then high-sensitivity nanoflow high-performance liquid chromatography (HPLC) electrospray tandem mass spectrometry, employing the complementary fragmentation approaches of collision induced dissociation (CID) and electron transfer dissociation (ETD). It also develops and maintains a free public website of software tools for analysis of large scale proteomic data sets called Protein Prospector (prospector.ucsf.edu). This toolbox is constantly adapted to accommodate new data analysis strategies for protein and PTM identification and site-specific quantification.

Current Research

Development of improved affinity approaches for selective enrichment of specific modifications. Development of approaches for studying the targets of specific enzymes or signaling pathways. Investigation into the use of complementary fragmentation approaches for PTM site identification and relative quantification. Application of new methods to study cross-talk between different PTMs on both the same and different proteins, in order to decipher dynamics of protein complexes and the function of regulatory systems. Development of improved data analysis tools, including the ability to compare or merge data from different experiments, to discover unexpected new post-translational modifications or to report quantitative measurements of peptide and site-specific PTM levels.

Resource Capabilities

Instruments

Thermo LTQ-Orbitrap electrospray hybrid linear ion trap and orbitrap instrument with option for ETD fragmentation, Thermo LTQ-FT electrospray hybrid linear ion trap and ion cyclotron resonance instrument with option for ECD fragmentation, Sciex QSTAR Elite, XL and Pulsar electrospray quadrupole orthogonal acceleration TOF mass spectrometers, ABI 4700 Proteomics Analyzer MALDI TOF TOF platform with 24-plate cassette sample-loading system, and Sciex API 300 electrospray triple quadrupole mass spectrometer. GE Healthcare Akta Purifier HPLC/FPLC system for off-line sample separation and selective PTM enrichment. Waters NanoAcquity ultra-performance liquid chromatography (UPLC) systems for high resolution nanoflow separation online to mass spectrometric analysis.

Special Features

Expertise in analysis of post-translational modifications and quantitative analysis with a focus on epigenetics. ProteinProspector data analysis tools, that allow comprehensive analysis and interpretation of all types of mass spectrometry-based proteomic data sets.