Proteomics

Proteins are the building blocks of life. Proteomics develops and implements advanced analytical technologies to study them.

Technology to drive breakthrough science

The Proteomics Core innovates, develops, and implements advanced protein analytical technologies (including quantitative proteomics, post-translational modifications, protein dynamics, and biomarker discovery) to advance basic biology and biomedical research. Staff in the Proteomics Core engage in many collaborative projects and are involved in worldwide mass spectrometric studies, as well as software development. Many different workflows are supported at our facility or can be developed together to support biological projects with innovate technologies to gain insights into molecular details in a system-wide approach.

  • Birgit Schilling, PhD . Director

    Birgit Schilling, PhD, is the director of the Proteomics Core and an Assistant Professor at the Buck Institute. She received her diploma and PhD in chemistry from the University of Hamburg and Clausthal University of Technology in Germany and did a postdoctoral fellowship with professors Al Burlingame and Brad Gibson at the University of California, San Francisco. Dr. Schilling joined the Buck Institute Proteomics Core in 2000 and has more than 25 years of experience in mass spectrometric (MS) technologies. She specializes in quantitative proteomics in the context of aging as well as MS method and workflow developments, such as for post-translational modifications, protein secretomes, exosomes, biomarkers, protein turnover, and proteostasis. She is a leader in the field of applying novel MS scan types, such as data-independent acquisitions (DIA) and parallel reaction monitoring (PRM), and corresponding data processing. Dr. Schilling oversees all proteomics projects and coordinates all collaborations.

  • Natan Basisty, PhD . Postdoctoral Research Fellow

    Natan Basisty is a postdoctoral fellow who joined The Buck Institute in 2015. He received his Ph.D. in Pathology and B.S. in Biochemistry from the University of Washington. He has been developing and applying mass spectrometry approaches to study the role of proteins and cellular protein quality control in health and aging for over 7 years. His current research focuses on discovering biomarkers of cellular senescence and developing translationally relevant approaches to study senescent cells.

    NBasisty@buckinstitute.org

  • Anja Holtz . Research Associate

    Anja Holtz attrended the University of Minnesota and graduated in 2017 with a BS in genetics, cell biology and development as well as ecology, evolution and behavior. Since then she worked at the Masonic Cancer Center doing breast cancer research for a year until she joined the Buck Institute in the summer of 2018. Anja has been extremely interested in genetics ever since the Human Genome Project was first publicized.

    AHoltz@buckinstitute.org

  • Xueshu Xie, PhD . Postdoctoral Research Fellow

    Xueshu received her Ph.D. degree in Medical Science from Karolinska Institute, Sweden under the guidance of Prof. Roman Zubarev. She joined the Schilling lab at the Buck Institute as a postdoc in June 2018. Xueshu has a strong interest in applying mass spectrometry-based proteomics to solve biological questions. Her current research is focused on studying protein posttranslational modifications (acylation, phosphorylation), protein aggregation and protein-protein interactions.

    XXie@buckinstitute.org

Protein expression changes

  • Precise quantification
  • High throughput of MS quantifying ~5000 proteins per acquisition
  • Technology development
  • State-of-the-art label-free workflows (data-independent acquisitions)

 

Protein networks

  • Protein-protein interactions
  • Immunoprecipitations

 

Biomarkers of aging and disease

  • Processing of biofluids, plasma, exosomes, synovial fluid
  • Protein secretion into biofluids from diseased tissues
  • Clinical sample sets

 

Protein turnover

  • Changes in protein synthesis and degradation
  • In-depth analysis of protein half-life and protein flux

 

Post-translational modifications

  • Dynamic regulation of PTM: phosphorylation, acetylation, succinylation, malonylation, ubiquitination, AGES, etc.
  • Affinity enrichments
  • Optimized for low sample material (from tissues)
  • PTM site stoichiometry

 

Software development

  • Custom software for data processing and reports
  • Skyline (MacCoss, U.Washington)

Many different types of analysis and projects can be processed in the Proteomics Core. Mass spectrometric workflows include data-dependent acquisitions (DDA) for protein discovery and identification; data-independent acquisitions (DIA) for comprehensive sampling of the proteome and accurate relative quantification; and targeted, hypothesis-driven proteomics experiments applying selected reaction monitoring (SRM) and high-resolution parallel reaction monitoring (PRM). Typical mass spectrometric experiments are listed below:

  • Protein identification
  • Quantitative proteomics assessing differential protein expression and relative changes of proteins when comparing different experimental conditions
  • Analysis of post-translational modifications (PTM), such as phosphorylation, acylation, ubiquitination, etc., including PTM crosstalk
  • Affinity enrichments
  • Protein-protein interaction networks
  • Protein turnover, protein half-life, proteostasis
  • Protein aggregation
  • MS of biofluids (e.g., plasma, urine) for biomarker analysis of aging and disease
  • Protein secretomes, exosomes, surfaceomes

Mass spectrometric instrumentation

The instrumentation at the Buck Institute Proteomics Core features mass spectrometers with overall high sensitivity and very high scan speed, as well as a large dynamic range that allows us to collaborate on a wide range of biological projects and questions that investigators may have. Different instruments offer different scan types, and our lab has specialized in data-independent acquisition (DIA or SWATH), which enables high-throughput mass spectrometry with measurement and quantification of up to 5,000 proteins in a single acquisition.

 

TripleTOF 6600 quadrupole time-of-flight (QqTOF, SCIEX) with 2D-nano LC system (Eksigent)

The TripleTOF 6600 is an orthogonal quadrupole time-of-flight mass spectrometer with high-resolution accurate mass technology. Optimized instrument control electronics in conjunction with patented LINAC collision cell technology deliver ultra-fast acquisition rates and high-resolution scanning. The TripleTOF 6600 is either operated in data-dependent acquisition (DDA) for discovery mass spectrometry or, more often, in data-independent acquisition (DIA/SWATH) for highly accurate protein quantification and determination of relative changes between different sample conditions. High-resolution parallel reaction monitoring (PRM) is used for sensitive and specific targeted quantification. Protein identification, PTM analysis, protein-protein interaction experiments, and so forth are routine on the TripleTOF 6600. Using DIA workflows, proteome-wide comprehensive protein quantifications can be performed in a high-throughput and accurate fashion.

 

TripleTOF 5600 quadrupole time-of-flight (QqTOF, SCIEX) with 2D-nano LC system (Eksigent)

The TripleTOF 5600 is an orthogonal quadrupole time-of-flight mass spectrometer with similar capabilities as the TripleTOF 6600. Together, they are a powerful suite of instruments for proteomics characterization of samples sets derived from tissues, cell lines, stem cells, and biofluids for analyzing different model organisms or human samples.

 

QTRAP 5500 triple quadrupole linear ion trap (QQQ, SCIEX) with 2D-nano LC system (Eksigent)

The QTRAP 5500 is a triple quadrupole linear ion trap for targeted proteomics analysis. The QTRAP 5500 allows for highly multiplexed selected reaction monitoring scan types (SRM), which provides highly sensitive and reproducible SRM-MS assays with a very good robustness when acquiring data from complex matrices (e.g., plasma). The QTRAP 5500’s high sensitivity quantification at high-throughput is key for several current projects.

 

vMALDI-LTQ (Thermo)

An intermediate-pressure matrix-assisted laser desorption/ionization (vMALDI) source is coupled with a LTQ linear ion trap. This instrument offers options such as multiple-stage mass spectrometry (MSn), which is highly relevant for structural elucidation of oligosaccharide and complex lipid structures.

Buck Institute Quantitative Proteomics Courses:

The Buck Institute for Research on Aging and the Skyline Team are pleased to co-announce the 4th Buck Institute Targeted Proteomics Course on March 18 – 22,  2019 in the Northern San Francisco Bay Area, California (Novato). 

The course schedule will address emerging quantitative proteomics strategies.  This will include the use of Skyline in the context of different quantitative targeted workflows, assay development, generation of acquisition methods, processing of quantitative data sets, as well as using statistical and R software packages and tools in Skyline.  Data examples will cover high through-put SRM, MS1 Filtering, parallel reaction monitoring (PRM) and data-independent acquisition (DIA/SWATH).  Data examples will range from analysis of posttranslational modifications, work with human plasma for biomarker analysis and projects involving protein-protein interactions. In addition, small molecule Skyline features and applications will be presented.

The instructor list includes researchers and software developers with a wealth of combined experience in targeted and quantitative proteomics, and both using and creating Skyline to meet the needs of this research approach.

Course Dates:

March 18-22, 2019

April 2–6, 2018

February 27–March 3, 2017

Please contact as us for more detailed information on the core’s mass spectrometric capabilities, services, and rates.

 

Birgit Schilling, PhD

Research Associate Professor

Director

415-209-2079

BSchilling@buckinstitute.org

 

Anja Holtz

Research Associate

415-209-2000 x6746

AHoltz@buckinstitute.org

 

Samah Shah

Research Associate

415-209-2000 x6710

SShah@buckinstitute.org

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