TECHNOLOGY MODULES
We see the list of tasks of the technology development group as dynamically
changing in response to the demands of the Biology Working Groups. Over the duration of
the Center, new technology modules will be conceived and some of the initial ones will either be
completed or phased out in response to ever-evolving requirements.
Technology Module A: Solid-phase stable isotope tag transfer chemistry
- W. Andy Tao, P.I.
The objective of this module is to develop automatable and automated
procedures for protein processing and stable isotope tagging. During the
first period of funding, we will establish and validate experiments that will
enable us to test different isotope tags and cleavable linkers, and start to
systematically explore different chemistries. In years 2 and 3, the
different chemistries will be optimized and commercialized.
Technology Module B: Selective isolation and stable isotope tagging of
phosphorylated peptides
- W. Andy Tao and Yong Chi, P.I.s
The objective of this module is to develop a new technology for the
systematic and quantitative analysis of protein phosphorylation on a
proteome-wide scale. During the first year of funding, we will establish and
validate experiments that will enable us to selectively isolate and isotope
tag phosphorylated peptides from complex mixtures. Initially, phosphopeptides
containing SH groups will be tested building on the protocols developed in
Technology Module A. In years 2 and 3, the analyses will be extended to use
NH2-specific peptide trapping methods.
Technology Module C: Selective isolation and isotope tagging of
peptides with lipid modifications
The objective of this module is to develop a new technology for the analysis
of protein lipid modifications on a proteome-wide scale. This project will
build on the development of the solid-phase isotope tag strategy that is the
subject of Technology Module A. No activities are planned for the first two
years.
Technology Module D: Preparation of stable isotope tagged peptides for
quantitative analysis of protein complexes
- Jeff Ranish, P.I.
The objective of this module is to develop a new technology based on
quantitative proteomics for the systematic and conclusive analysis of protein
complexes, their components, stoichiometry, and dynamics of composition.
During the first period of funding, we will establish basic protocols for the
quantitative analysis of the components of protein complexes. In the first
year, we will demonstrate that we can distinguish between specific and
contaminating components of the complexes and that we can detect changes in
abundance of complex components. The protocols will be transferred to the
high throughput facility (HTPF) and applied to biology working group projects.
In years 2 and 3, procedures to determine absolute quantification of complex
components and, therefore, the stoichiometry of complexes will be developed
and implemented.
Technology Module E: Development of multiplexed high throughput peptide
separation systems
- Mingliang Ye, Johan Malmstroem, P.I.s
The objective of this module is to develop a comprehensive peptide separation
platform for robust and reproducible peptide separations carried out at high
throughput. During the first funding period, we will determine the most
efficient way to increase sample throughput for proteomic analysis. The most
efficient methods will be further developed in years 2 and 3. The research
will proceed along two tracks: the first is based on ESI-MS/MS and the
second is based on MALDI-MS/MS.
Technology Module F: Development of a mass spectrometric technology for
quantitative high throughput protein analysis
- Mingliang Ye, Johan Malmstroem, P.I.s
The objective of this module is to develop an analytical platform based on
MALDI tandem mass spectrometry for the quantitative analysis of complex
protein mixtures at high sample thoughput. In the first period of funding,
we will implement a system for high throughput peptide analysis based on
MALDI-TOF/TOF and MALDI-QTOF technology. In years 2 and 3, the technology
will be implemented in the HTPF and applied to projects of the BWG.
Technology Module G: Development of a suite of software tools for
protein identification and quantification using mass spectra and tandem mass
spectra
- Jimmy Eng, P.I.
The objective of this module is to develop and disseminate a suite of
software tools for the automated analysis of quantitative proteomics data. A
main benefit of this suite will be the ability to standardize results obtained
in different experiments, labs and centers, and therefore to make diverse
data sets comparable and portable. The development of software tools for
proteomics research is a top priority for the Center. In the initial phase,
tools for peptide and protein identification and quantification will be
concurrently developed as independent modules. After testing and validation,
the individual modules will be merged into an integrated system in years 2 and
3 of the program. To train scientists in the use of the tools, the Center
will periodically offer a training course.
Technology Module H: SBEAMS - A proteomics database
- Eric Deutsch, P.I.
The objective of this module is to develop a relational database for the
collection, storage and dissemination of proteomics data. In the initial
phase of this project, the SBEAMS database will be implemented and tested at
ISB as a research tool and as a tool to support the HTPF. In years 2 and 3,
the database will be continually in process and disseminated to other centers.
Technology Module I: Expression and purification of protein domains for
the selection of high affinity photo-aptamers
- Patrick Pedrioli, P.I.
The objective of this module is to develop reagents and technology required
to carry out quantitative protein profiling experiments using array technology.
In the initial funding phase, the contractual agreement with SomaLogic will
be finalized and an initial set of 5-10 proteins will be prepared for the
purpose of selecting apatamers specific for those proteins. In years 2 and 3,
the number of proteins will be ramped up.
Technology Modules Staff
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