# Presentation: 061424

## CBIIT Proteomics Projects

**May, 2008**

## Agenda

**CPAS – Computational Portal and Analysis System**
**CPAS-MART – BioMart module for CPAS **
**CPAS-Grid – caGrid enabled CPAS**
**Demonstration**

## CPAS

**CPAS**

## Developed by Fred Hutchinson Cancer Research Center
Mass Spectrometry experiments data
Proteomics Analysis Tools
Proteomics Repository for Mouse Proteomic Technology Initiative

**Mass Spectrometry experiments data**
**Proteomics Analysis Tools**
**Proteomics Repository for Mouse Proteomic Technology Initiative**

**CPAS**

**Notes:**
First release in 2006, CBIIT is running version 2.2
open-source, web-based analysis platform that organizes and annotates general biological experiments
peptide sequence database 
MASS Spectrometry experiments.
CPAS incorporates tools for proteomics analysis, such as X!Tandem search engine, the PeptideProphet and ProteinProphet.
CPAS can be switched to use other search engines, including Mascot and SEQUEST

## CPAS Application Architecture

-  Site Admin

- Data Storage (Relational Database + File System)

- Experiment Services (Shared Ontologies, XAR)

- Portal / Wiki

- Protein Services

- MS1

- MS2

- Experiment

- Sample

- Mouse

- = Shared services

- MS2Search

- = Modules

- Flow Cytometry

- Data Pipeline

- Study

- Query

**CPAS Application Architecture**

**Notes:**
consists of a core system of services that provide underlying system functionality such as data storage, security, web interface, query, experiment and protein services.
Modules are plugged into the core to provide data handling and analytical support
With this design, The CPAS system is easily extensible.
This architecture allows new modules to be added and integrated without having to modify the core system
CBIIT installation has additional module called MS2Search for Peptides Sequenece query.

## NCI-CPAS Home Page

- http://cpas.nci.nih.gov

**Notes:**
MS2 Statistics  - 2 years of data

Private and public access to browse data

security mechanism that allows only those with proper permission to access specific data

## Project, Experiment, Run

**Notes:**
CPAS use folder concept to store data.
The folders  are organized using Projects, Experiments and Runs hierarchy.

## Peptides in MS/MS Run

**Notes:**
This slide shows all the Peptides  for a MS2 Run

MS2 Run summary is displayed at the top, followed by are customizable view of peptides information
Predefined filters can be applied to the view

The column headings that appear in the display grids allow user to sort peptide list.

Peptides and Proteins columns are clickable.

Click the Peptide name will go to the Peptide Spectrum page, which displays the MS2 spectrum of the fragmented peptide. 

## MS/MS Spectrum

**Notes:**
Click the Peptide name to go to the Peptide Spectrum page, which displays the MS2 spectrum of the fragmented peptide. 

The graph shows RAW spectrum profile data, similar to DNA sequence database (Gene DB).

Click the Protein name to go to the Protein Details page, which displays information on that protein and the peptides that matched it.

## Protein Annotations

**Notes:**
Click the Protein name to go to the Protein Details page, which displays information on that protein and the peptides that matched it.

## NCI Implementation of Peptide Query

**Search performance**
**Blast algorithm**
**Query by Peptide sequence module **

**NCI Implementation of Peptide Query**

**Notes:**

People wants to see if a peptide exists in the current database

Blast algorithm – commonly use sequence matching algorithm
Performance is very good.

NCI’s installation has been customized to include Query by Peptides sequence search capability.
Use Blast as the underlying search engine

## Query By Peptide Sequence

**Notes:**
The Peptide sequence search is implemented under the MS2Search module.
User first selects which folder to search on
Type in any AMINO acids sequence to search on, select one or more subfolders
Any nested subfolders will also be included in the search.

Since we are using the Blast algorithm, search result usually displayed within  seconds

## CPAS Peptide Query Results

**Notes:**
Peptide sequence query results are grouped by Runs
Adapted similar interface as MS2 Run, 
results can be exported to various format, such as Excel

## CPAS MART

**CPAS MART**

## CPAS MART

**Need to create complex queries**
**More flexible filters**
**Subset of data fields can be selected to include in the query results**
**Results can be exported to files**
**Generic query services for CPAS data built upon BioMart version 0.6**

**Notes:**
We found out that sometimes we need to look at the proteomic data in different way other than grouped by MS2 Run.
There is need to ...
BioMart is a query-oriented data management system developed by the Ontario Institute for Cancer Research (OiCR) and the European Bioinformatics Institute (EBI). 

## CPAS Mart Architecture

**CPAS Mart Architecture**

**:**

**CPAS DB**
**exp, msruns****,**
**Prot etc..**

**XML**

**Configuration**

**MartBuilder**

**MartEditor**

**Mart** **Explorer**

**Mart** **Shell**

**CPAS Mart** **View**

**Schema**
**Transformation**

**dbSNP, **
**UniProt,**
**Ensembl etc**

**Public Data**

**Notes:**
Biomart comes with a set of tools, likes Mart Explorer, Mart Shell, Mart Builder, and MartEditor
Starting with MartBuilder to select what kind of data to expose in the current CPAS schema
A new CPAS Mart schema was created with data imported from CPAS schema.
MartEditor  is the tool to configure and customize the CPAS mart schema. e.g. create additional field 
Since it is a separate schema, it will not affect the original CPAS schema and application

Use Uniprot DB – IPI (international protein index)

## http://cpas-mart-stage.nci.nih.gov/ 

- CPAS MART

**Notes:**
The current CPAS Mart provides four datasets, namely Experiment Run, MS2 Run, Peptides, and Protein Sequence
User start a new search by specifying which dataset to search on
Then select one or more attributes for display
Optional  filters can be specified
Related datasets can be joined together.

## CPAS MART Results 

- CPAS MART Results

**Notes:**
Query results can be viewed online or exported to file in HTML, TSV,  Excel CSV, or TEXT formats
For complex query or query with large result sets, user can select Email Notification option.   The user will receive an email containing a link to download the query result.

## CPAS-Grid

**CPAS-Grid**

## CPAS-Grid (caGrid enabled CPAS)

**Made CPAS public data accessible thru the caGrid**
**caBIG silver-compliant experimental information**
**Used CPAS caBIG development kit and caCore SDK to generate caGrid service components and client API.**
**Used “Introduce” toolkit to package the components and deployment**

**Notes:**
Starting CPAS 2.1, it is caBIG silver-compliant

application programming interface to the principal objects (project, experiment, protocol, run, peptide) 

## How to access CPAS data thru caGrid

**Apache Tomcat 5.0.28**

**caGrid**** **
**Data and Query**
**Services**

**caGrid Portal (browser)**
_***or***_
**Application using caGrid API to Query CPAS caGrid Service**

**CPAS DB**

**Apache Tomcat 5.5.20**

**CPAS**** caGrid**
**Data Service**
**-----------------**
**CPAS Application**

** **

**Service**

** ****caGrid Index Server and Discovery Service**

**Notes:**
CPAS caGrid service provides a set of APIs for the project, experiment, protocol, run, peptide objects.
User can either use the APIs or the caGrid Portal to retrieve CPAS data.

Use the Index Server and Discovery Service to find out what kind of service is available and where the service is located.
User can submit a  CQL query thru the grid to the caGrid data and Query services for data mapping and transformation.
Object query will be formed and submitted to the CPAS data service.
Result Objects will be returned back to user

CQL - caGrid Query Language 

## http://cagrid-portal.nci.nih.gov/ 

_**[http://cagrid-portal.nci.nih.gov/](http://cagrid-portal.nci.nih.gov/)**_** **

- NCI caGrid Portal

**Notes:**
The caGrid Portal contains all the Data and Analytical services that registered to NCI.
The home page shows a graphic representation where each service is located
Clicking the icons will show you the hosting center information and the services it provides.

User can use the TOOLS menu to browse the available services or search for a particular one.

## Submit Query using NCI caGrid Portal 

- Submit Query using NCI caGrid Portal

**Notes:**
Left side shows the summary for the CPAS caGrid service,    Domain model etc.

Right side is the Data Services Query box.
User can submit CQLs to retrieve CPAS data, the current example shows ....

## Results Displayed using NCI caGrid Portal 

- Results Displayed using NCI caGrid Portal

**Notes:**
Results can be exported to Excel format

## Demonstration

**Demonstration**