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Tutorial: How to Use this Site (4 minutes/2.7M)

This tutorial demonstrates through a sample use case the most common functions of this Website.

Use Case: retrieve Salmonella typhimurium proteins identified by mass spectrometry and linked to the Immune Epitope Database (IEDB); one such peptide sequence will be identified and its mass spectrometry data downloaded.

1. Retrieve all Salmonella typhimurium proteins
2. Retrieve those identified by mass spectrometry
3. Keep only Salmonella typhimurium proteins linking to the IEDB (IEDB ID not null)
4. Identify a specific peptide sequence
5. Download mass spectrometry data

Tutorial: Basic Text Search (2 1/2 minutes/2.9M)

This tutorial demonstrates a basic text search to make protein discoveries.

Use Case: discover functions of a hypothetical protein to demonstrate a simple text search.

1. Retrieve all Vibrio cholerae proteins
2. Retrieve only proteins with structures (PDB not null)
3. Link to iProClass shows hints on Classification
4. Link to PIRSF gives family information that hints on its function
5. User may continue with the research on this hypothetical protein

Tutorial: Data Exploration (1 1/2 minutes/3.4M)

This tutorial demonstrates the integration capabilities of the NIAID Proteomics Website.

Use Case: find a common set of Mus musculus proteins identified by microarray and mass spectrometry under Bacillus anthracis and Salmonella typhimurium infection conditions.

1. Retrieve all Mus musculus (host) proteins
2. Retrieve proteins identified under both conditions of Bacillus anthracis and Salmonella typhimurium infection experiments
3. Select data from microarray

Tutorial: How to Purchase a Reagent (3 minutes/2.4M)

This tutorial demonstrates how to search, save, and purchase a specific reagent.

Use Case: purchase and save data for a Yersinia pestis clone researched by Myriad Genetics.

1. Retrieve all reagents of the clone Data Type
2. Keep only reagents researched by Myriad Genetics
3. Keep only reagents of the organism Yersinia pestis
4. Download reagent information for reanalysis
5. Purchase a reagent for further investigation