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SUMS Research Applications Symposium

October 29, 2015

Location: Arrillaga Alumni Center [map, transportation & parking directions]
Admission: Free


A symposium for users of mass spectrometry resources as well as those interested in finding out more about applications of the technology. The Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS) is an annual opportunity for Stanford and community scientists to meet, mingle, and learn about research resources and ongoing mass spec related research at Stanford.

Keynote Speaker: Carolyn R. Bertozzi, PhD

Carolyn R. Bertozzi


We are delighted to have Carolyn R. Bertozzi give the keynote presentation.  Prof. Bertozzi is renowned for both her research and teaching, and has moved to Stanford after 18 years at UC Berkeley.  She is credited as founding a field called bioorthogonal chemistry, which allows researchers to chemically modify molecules within living cells. Her lab is developing a mass spec-based isotope-targeted glycoproteomics (IsoTaG) platform.  Through collaborations at Stanford, Prof. Bertozzi is hoping to bring her field closer to being clinically relevant for people.



8:00am Registration/Breakfast
Exhibits (all day)
8:30am Introduction and Welcome

Scientific Session I: Seed Grant Projects

8:40am Identifying protein quality control substrates with mass spectrometry
Prof. Onn Brandman, PhD, Department of Biochemistry, Stanford University Medical Center
9:00am Seeing Impurity Through MALDI MS: Optimization of Living Polymerization for the Synthesis of Well-Defined Polymer Architectures
Prof. Yan Xia, PhD, Department of Chemistry, Stanford University
9:20am RNA-Protein Interactions in Oligodendrocyte Development and Myelination
Meng-meng Fu, PhD, Department of Neurobiology, Stanford University Medical Center
9:40am Role of Telomere Erosion in Lethal Cardiomyopathy in Duchenne Muscular Dystrophy
Alex Chang, PhD, Department of Microbiology & Immunology, Stanford University Medical Center

hiPSC-Cardiomyocytes to Screen Variants Predictive of Doxorubicin Cardiotoxicity
Prof. Daniel Bernstein, MD, Department of Pediatrics - Cardiology, Stanford University Medical Center

10:20am Comparative Proteomics of Primary Cilia using APEX-based Proximity Labeling
David Mick, PhD, Department of Molecular & Cellular Physiology, Stanford University Medical Center
10:40am Morning Break


Chemical Glycoproteomics
Prof. Carolyn R. Bertozzi, PhD, Department of Chemistry, Stanford University

12:00pm Lunch, Poster Session

Sponsor Seminars

  Adding Dimension to Applications using Ion Mobility (abstract)
Caroline S. Chu, PhD, LC/MS Application Scientist, Agilent Technologies, Inc.
  Applications for targeted metabolomics: Overview on mass spectrometric based metabolomics kits and services (abstract)
Ralf Bogumil, PhD, Regional Director North America
Maria Chiam, BPharm, MBA, Business Development West Coast, Biocrates
Life Sciences

Exploring monoclonal antibody glycan structures (abstract)
Shuai Wu, PhD,  Application Scientist, Bruker Daltonics


Applications in Full Spectrum Molecular Imaging and Rapid Evaporative Ionization Mass Spectrometry (REIMS) (abstract)
Bindesh Shrestha, PhD, Senior Application Support Scientist, Waters Corporation

2:00pm Afternoon Break

Scientific Session II: Faculty Research

2:20pm Pathway Illumination for Disease Research - Psychiatric Disorders and Antidepressant Treatment Response
Prof. Chris Turck, PhD, Max Planck Institute of Psychiatry, Munich
2:55pm Uremic Solutes from Gut Microbes
Prof. Tim Meyer, MD, Department of Nephrology, Stanford University Medical Center
3:30pm Understanding Signaling Pathways in Primary Cilia via Protein-Protein Interaction Networks and Systems Analysis
Prof. Peter Jackson, PhD, Department of Microbiology & Immunology, Stanford University Medical Center
4:05pm Reception and Final Raffle




Agilent Technologies Logo Biocrates Logo Bruker Logo Waters Logo


AB Sciex Logo Perkin Elmer Logo Promega logo
  Thermo Scientific Logo Veritomyx logo


Cell Signal Logo Proteome Software Log SageN Logo



Sponsor Seminars, 1-2pm. Select during registration

Agilent Technologies

Adding Dimension to Applications using Ion Mobility 
Caroline S. Chu, PhD, LC/MS Application Scientist, Agilent Technologies, Inc.

Mass spectrometry has now been a routine bio-analytical technique used across different applications.  With the introduction of ion mobility, a new dimension of information is now available for each target analyte across applications.  In this discussion, we will highlight the different types of applications where ion mobility provides a new dimension of information using the Agilent 6560 IM-QTOF MS.  Applications will including protein characterization encompassing protein structure by native MS, proteomics, and post-translational modifications such as glycan analysis.  In addition, we will highlight the added dimension ion mobility provides for biological applications such as metabolomics. (back to top)

Applications for targeted metabolomics: Overview on mass spectrometric based metabolomics kits and services
Ralf Bogumil, PhD, Regional Director North America
Maria Chiam, BPharm, MBA, Business Development West Coast, Biocrates 
Life Sciences

This workshop discusses the application and approaches of targeted metabolomics  and the problem solving products and services for integrating metabolomics to proteomic, transcriptomic, and metabolomic information providing researchers a better understanding of cellular biology. Biocrates ( enables immediate identification and absolute quantification of up to 630 endogenous metabolites of different classes. Through the use of targeted metabolomics (FIA-MS/MS and LC-MS/MS quantification of metabolites), Biocrates can enable researchers to study metabolic comparisons of different biological samples and thus highlight differences in metabolite levels. This is of high value in a variety of applications such as  improving biomarker identification (for monitoring disease status and drug efficacy) or to monitor toxicity. (back to top)

Exploring monoclonal antibody glycan structures
Shuai Wu, PhD, Application Scientist, Bruker Daltonics

Monoclonal antibodies produced in mammalian expression systems are post-translationally modified by N-linked glycosylation, and the type and termination of the peptidoglycan affects both antibody pharmacokinetic properties and immune signaling functions.  Thus, it is essential to understand which glycans are present.  Bruker provides a comprehensive solution for glycan, glycopeptide, and glycoprotein analysis using ESI-QTOF and LC MALDI. For glycopeptides, Bruker QTOF has developed a CID method that uses 2 levels of collision energy to produce all the fragments needed for ID of the glycan and the peptide. The glycan module - GlycoQuest - inside ProteinScape has highly linked interactive viewers for convenient result validation and ability to see the identified composition for released glycans or (in the case of glycopeptides) the peptide sequence and the glycan composition. To simplify the data processing and visualization of results, the spectra at both energy levels are combined to produce a single spectrum containing all the information present in both sub-spectra. The energy of the MALDI ionization is sufficient to cleave glycan rings, producing the fragments that are critical to positively identify the structure.  The spectra can be search and identity assigned automatically with ProteinScape. (back to top)

Applications in Full Spectrum Molecular Imaging and Rapid Evaporative Ionization Mass Spectrometry (REIMS)
Bindesh Shrestha, PhD, Senior Application Support Scientist, Waters Corporation

Full spectrum molecular imaging is a comprehensive mass spectrometry imaging platform for obtaining spatio-molecular information from biological samples. Matrix-assisted laser desorption/ionization (MALDI), desorption electrospray ionization (DESI), ion mobility separation, and informatics workflow are incorporated into a single instrument platform (e.g., SYNAPT G2 Si) to get enhanced molecular distributions in tissues. In traditional mass spectrometry imaging, the molecular information is often deduced from the mass-to-charge ratios of the ions, often ignoring the presence of isobaric ions, such as structural isomers. Traveling wave ion mobility separation (TWIMS) is able to sort out isobaric species using the difference in their drift times, as well as, provide orthogonal molecular information using their collision cross-sections (CCS).
Rapid Evaporative Ionization Mass Spectrometry (REIMS) is a novel hand-held ambient ionization mass spectrometry (AIMS) sampling device. REIMS samples tissue by vaporizing with a localized high frequency electric current on its surface. The sampled vapors are ionized by the heated impactor surface and analyzed by a mass spectrometer. Selected applications demonstrating the unique capabilities of full spectrum molecular imaging and REIMS will be discussed in the seminar. (back to top)