SBEAMS - Proteomics Tutorial
Eric Deutsch


If you have suggestions or bug reports for this tutorial, please email Eric Deutsch.

  1. Login:
  2. 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.
  3. 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
  4. 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.
  5. 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'
  6. 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:
        1. Click i balloon
        2. Expand GO, Molecular Function
        3. Click on 3
        4. Click 'Apply Annotation' to all Nodes.
        5. Click on Go Molecular Function (level 3) on right
        6. Click Layout
        7. Expand Go Molecular Function (level 3) on right
        8. Click on individual GO categories and see them highlighted
        9. Click on 'hydrolase' and then right click on graph and see attributes
        10. Exit Cytoscape. Tomorrow will be all Cytoscape!
  7. 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].
  8. 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.
  9. 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.