SBEAMS - Proteomics Tutorial
Eric Deutsch
If you have suggestions or bug reports for this tutorial, please email Eric Deutsch.
- Login:
- Go to Proteomics Module Home Page and test controls
- Current Project
- Projects You Own
- Projects You Have Access To
- Also note sections 'Recent Query Resultsets within the Proteomics Module' and 'Other Links'.
- Click on project names to switch current projects
- Switch Group and Project at the top and then finally end up at 'Proteomics_user' or 'Proteomics_readonly' and Project is 'mmarelli - Peroxisomal Proteomics'.
- Click on 'Current Project' hyperlink to view project attributes
- Click BACK and then [View/Edit] under Experiments. This page allows one to add annotation to an individual experiment.
- Add your own Project if you don't already have one
- Click 'My Home' in upper left
- Under Projects You Own, click [Add new project] or if you already had an SBEAMS project and didn't create a new one, edit the existing one (again, by '[View/Edit]') and UPDATE.
- Fill out the form for some real project and INSERT
- Click on 'My Home' and make sure it's there. Make it the active project.
- Click [View/Edit], adjust the description a little, and UPDATE
- If you already had an SBEAMS project and didn't create a new one, edit the existing one (by '[View/Edit]') and UPDATE
- Register a new experiment
- Make your new/existing Project the Current Project
- Under Experiments, click [Register another experiment]
- Fill out the required and optional information to register the 210-spectrum dataset. Use the 'mmarelli - Peroxisomal proteomics' experiment for experimental configuration as an example if you wish.
- INSERT
- Click back on My Home and verify that all went in okay.
- At present, you cannot load your data. You would email Eric Deutsch and some time later, your data would magically appear in the database.
- Explore the 'mmarelli - Peroxisomal proteomics' project/experiment
- Set the Current Project to 'mmarelli - Peroxisomal proteomics'
- View project and experiment attributes
- View Fractions (MS Runs) (scroll down!!)
- Click on some TIC Plots in the table
- Click on an MS Run Summary and then the image and expand the image.
- Go back to My Home and click on 'P > 0.9' for 'Peroxisomal proteomics'
- Browse this dataset using hyperlinks on left navigation bar
- Choose Summarize Fractions
- Choose 'mmarelli - Peroxisomal proteomics' experiment or project and view
- Choose Browse Search Hits
- Select 'mmarelli - Peroxisomal proteomics' experiment
- P > 0.9
- QUERY
- Click on all hyper links across the table
- Re-sort by Xcorr descending. Re-sort by precursor mass, Ions, etc.
- Page through resultset
- View in Excel, XML
- Make a histogram of Precursor m/z, then % ACN
- Make a scatter plot of % ACN vs EstRT(min)
- Click Display Option: Show SQL and QUERY
- Choose Summarize over Proteins/Peptides
- Select 'mmarelli - Peroxisomal proteomics' experiment
- P > 0.9
- QUERY
- In Display options, show GO columns & Show SQL and QUERY
- Click on all hyper links across the table
- Click on Display option: Group By Peptide and QUERY
- Click on the 28 next to FOX2 LCTPTMPSNGTLK and examine
- Choose Compare Experiments
- Select jranish - gricat experiment
- Also CTRL Select 'mmarelli - Peroxisomal proteomics' experiment
- QUERY
- Examine differences between experiments and summary table
- Find overlaps by select Full Detail and '>0' for both Exp 1 and 2
- Group by peptides and examine
- Choose Browse Biosequences
- Choose Browse Possible Peptides
- 'Select Yeast ORF' Database
- In 'Gene Name constrait', type: PEX%
- Select 'Cysteine Containing' and 'Unique'
- QUERY
- Choose Protein Summary (ProteinProphet output)
- Select 'mmarelli - Peroxisomal proteomics' experiment
- Protein Group Probability > 0.7
- QUERY
- Choose 'Full Detail' for 'Input Form Format'
- Enter %perox% in cellular component
- QUERY
- Remove %perox% and reQUERY
- Re-sort by descending Probabilty
- [View this Resultset with Cytoscape]
- Within Cytoscape:
- Click i balloon
- Expand GO, Molecular Function
- Click on 3
- Click 'Apply Annotation' to all Nodes.
- Click on Go Molecular Function (level 3) on right
- Click Layout
- Expand Go Molecular Function (level 3) on right
- Click on individual GO categories and see them highlighted
- Click on 'hydrolase' and then right click on graph and see attributes
- Exit Cytoscape. Tomorrow will be all Cytoscape!
- Choose Publications and explore. Add your favorite Proteomics paper if it's not there yet. Enter the PubMed ID and press [TAB]; if the page doesn't automatically refresh, click [REFRESH].
- Choose Proteomics Toolkit and explore. Fragment peptide: PYLVSPVAFK. Find all instances of this peptide in the 'Peroxisomal proteomics' experiment and compare fragmentation list in spectrum view.
- Now use the interface to answer these questions:
- How many cysteine-containing peptides does the PET9 protein have?
- How many of these are observed in 'Peroxisomal proteomics'
- Explain the difference between these results
- How many peroxisomal proteins were identified in the 'Peroxisomal proteomics' Protein Summary (ProteinProphet)?
- Of all the (GO-annotated) yeast peroxisomal proteins, how many were identified in pxproteomi, jranish-gricat, both, and how many not seen at all? (hint: remove default '# of matches constraint')
- Why so few peroxisomal proteins in gricat?
- Create a list of a few proteins not currently annotated as peroxisomal but that might be peroxisomal based on a comparison of identifications in 'Peroxisomal proteomics' and gricat. Email to Eric Deutsch the URL for your full query or resultset.
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