1.1 System Overview

The Integrated Proteomics Pipeline (IP2) is a proteomics data analysis platform that has been designed by a core bioinformatics team. We understand that you want to receive your results fast without trading accuracy. Consequently, the IP2 has been designed to easily handle high-throughput proteomics data with a comprehensive interface that gives you confident results. You will also benefit from our expert customer support, which is free for the first year with the purchase of the IP2. The IP2 can also be integrated with our cloud computing service that eliminates the need for computational clusters and increases the data analysis speed.

There are three options to use the IP2 platform. Sometimes, you want to combine more than one option, so depending on the amount of data, you can switch to a different option. For example, you can run a single box in general without paying a cloud or cluster fee. When you have to analyze large data in a timely manner, you can select an option to submit jobs to either cluster or cloud.

By using the IP2 your laboratory will benefit from: One easy to use interface Project organization tools Protein database tracking and management Protein identification Quantification analysis (Any types of labeling strategies including SILAC, 15N, TMT, iTRAQ, etc. and label-free analysis) Clustering proteins by their expression changes (TBA) Gene ontology analysis) Statistical analysis for comparing multiple experiments PTM analysis Cloud computing service
The IP2 has been developed as a server-side platform, so it is operating system independent. Users need a web browser (e.g. firefox, IE, safari, Chrome, etc.) to access the IP2 system. However, some of the graphical user interfaces require the Java be installed on the client computer. Java is freely available to download and install at java.com.

Case 1: Single (standalone) IP2 server

Ideal for a small or moderate amount of data. Simple one box makes it simple and easy to maintain.

Case 2: IP2 with local cluster

Ideal for a large amount of data. This option is suitable for using an existing cluster or building a new cluster. Users can start a small number of cluster nodes, and gradually add more nodes later.

Case 3: IP2 with cloud

Ideal for analyzing data on demand. This is maintenance-free for computational nodes.

By using the IP2 your laboratory will benefit from:

• One easy to use interface
• Project organization tools (easy to organize large data)
• Project Sharing with other IP2 users or collaborators
• Protein database tracking and management
• Protein identification
• Quantification analysis (Any types of labeling strategies including SILAC, 15N, TMT, iTRAQ, etc. and label-free analysis)
• Clustering proteins by their expression changes (TBA)
• Comprehensive PTM analysis tools
• Gene ontology analysis
• Compare multiple samples to quickly and confidently find interesting proteins on both identification and quantification level
• A number of statistical analysis tools
• A number of visualization tools
• Customize the IP2 with your own tool with IP2 development kit (IDK)