patricia hernandezgeneva, 28 th september 2006 swiss bio grid: proteomics project (pp)
TRANSCRIPT
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Patricia HernandezGeneva, 28th September 2006
Swiss Bio Grid: Proteomics Project (PP)
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Definition:
Set of technologies and methodologies for large-scale studies of proteins identification / characterization / quantification
Context: Proteomics
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Definition:
Set of technologies and methodologies for large-scale studies of proteins identification / characterization / quantification
Typical proteomic study:
identify proteins that are differentially expressed between two samples (e.g. normal vs disease state)
Context: Proteomics
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Definition:
Set of technologies and methodologies for large-scale studies of proteins identification / characterization / quantification
Typical proteomic study:
identify proteins that are differentially expressed between two samples (e.g. normal vs disease state)
Technology:
mass spectrometry (MSMS) = mass measurement of protein fragments
Context: Proteomics
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Identification of proteins: principle
Many available tools; all work in the same way a LIST OF MSMS SPECTRA processed sequentially
a LIST OF POSSIBLE SOLUTIONS e.g. a list of known protein sequences
thousands to miostens to thousands
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solutions are (sequentially) evaluated against the spectra using a COMPARISON FUNCTION
some display (OUTPUT) of the identified proteins (with/without additional features such as statistics, result export, etc.)
Identification of proteins: principle
thousands to miostens to thousands
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Key idea:
Give access through a unique web portal to several spectrum analysis software in a workflow-oriented data analysis platform.
the swissPIT platform
Key idea and main objectifs of the PP
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Key idea:
Give access through a unique web portal to several spectrum analysis software in a workflow-oriented data analysis platform.
the swissPIT platform
Main objectifs:
- increase the coverage of identified proteins
- automatise analysis workflows
- provide a environment for parameter optimisation studies and for benchmarking
Key idea and main objectifs of the PP
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Interaction with the user:
MSMS data upload
choice of workflows and parameter configuration
result visualisation
data/result sharing
swissPIT overview: three distinct parts
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Execution of the analysis workflow selected by the user
data exploitation or high-throughput centered workflows
task-specific workflows (=personalized for a given lab)
swissPIT overview: three distinct parts
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Easy parallelisation
In a workflow, several analysis tools may be called in the same time (and independently)
For a given identification tool, the spectrum list and/or the db can be splitted into bundles and each bundle analysed independently
swissPIT overview: three distinct parts
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Use of distributed resources
Each site decides what databases and tools to install and maintain.
Corresponds to the « reality ». Research groups and proteomics facilities are geographically scattered and need to collaborate.
swissPIT overview: three distinct parts
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Current status of swissPIT
Web-based interface
4 protein identification tools Phenyx X!Tandem Popitam InsPecT
2 protein sequence databases uniProtKB/swissProt (>230’000 entries) uniProtKB/trEMBL (> 3’180’000 entries)
swissBioGrid compatible (submission to a grid is transparent for the user)
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User layer System layer
Current status: swissPIT from inside
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User layer System layer
Current status: swissPIT from inside
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User layer System layer
submit
mgf
Current status: swissPIT from inside
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User layer System layer
submit
mgf
Current status: swissPIT from inside
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User layer System layer
submit
mgf
Grid/cluster
Current status: swissPIT from inside
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User layer System layer
submit
mgf
Grid/cluster
Current status: swissPIT from inside
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http://swisspit.cscs.ch/
usernamepwd
Current status: swissPIT from outside
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some globalparameters
Current status: swissPIT from outside
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List of software that are installedCheck/uncheck boxes to select software to be run on the data
Current status: swissPIT from outside
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Click on link to display and configuresoftware specific parameters
Current status: swissPIT from outside
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Click on link to display and configuresoftware specific parameters
Press to run the software
Current status: swissPIT from outside
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Go to the user spaceBrowse old/new project
Current status: swissPIT from outside
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Results are visualized in native format raw text for Popitam, InsPecT XML with style sheet for X!Tandem advanced java interface for Phenyx
Current status: swissPIT from outside
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Code improvement improve readability and maintainability of code
Upcoming work
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Code improvement improve readability and maintainability of code
Standardisation unify parameters as much as possible display results in one format
Upcoming work
![Page 29: Patricia HernandezGeneva, 28 th September 2006 Swiss Bio Grid: Proteomics Project (PP)](https://reader036.vdocuments.site/reader036/viewer/2022062722/56649f325503460f94c4f0fe/html5/thumbnails/29.jpg)
Code improvement improve readability and maintainability of code
Standardisation unify parameters as much as possible display results in one format
Workflows find a way to implement workflows using xml
configuration files
Upcoming work
screen for unsuspected modificationsscreen for proteinsremove spectra with low peak statistics
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Ron Appel
Patricia Hernandez
Celine Hernandez
Andreas Quandt
Marc Tuloup
Pierre-Alain Binz
Markus Müller
Alexandre Masselot, Nicolas Budin
Vital-it team + Bruno Nyffeler
Peter Kunszt, Sergio Maffioletti, Arthur Thomas
Involved people, acknowledgments
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Thankyoufor
yourattention
Involved people, acknowledgments