Things you can check out:
Mass Spec Data Example:
*MASCOT example: http://www.matrixscience.com/cgi/master_results.pl?file=../data/F981122.dat
See the AAs they identified for each protein highlighted in red.
How to deal with large datasets? -- Organelle Proteomics Sites
Nucleolar Database (Angus Lamond Lab): http://www.lamondlab.com/NOPdb/NPDdatabase.htm
(search function is down for update in 2011, but check out how they sorted using GO terms)
Organelle DB: http://organelledb.lsi.umich.edu/
Labs who use MudPIT:
Yates Lab at Scripps: http://fields.scripps.edu/
Got MudPIT? article: http://www.dddmag.com/MudPIT-combines-LC-and-MS.aspx
Running a protein gel
Lab 7: Proteomics
Sample questions you could find out using Uniprot:
Any isoforms? If so, what is the difference between the them?
Gene Ontology? (Biological Process, Cellular Component, Molecular Function)
Protein-protein or binary interactions?
Questions you could ask using Expasy?
Where does trypsin cut your protein? How many peptides are formed when you cut with trypsin?
What is it's isoelectric point?
What is it's molecular weight?
Protein domain structure/Sequence Annotation
Do you have a protein domain structure for your protein yet? (you should!)
If not, you can use UniProt link out to SMART, PROSITE or PFAM by clicking on [Graphical View] under
Family & domain databases
You can use the information in the sequence annotation section to draw where your protein domains are as well.
You can also use Powerpoint or any other image rendering program like Adobe Illustrator or Photoshop to draw.
--if you want me to show you how to do this--just ask!
Post Translational Modifications
Does your protein have any post-translational modifications (PTMs)?
Predicting Subcellular Location
Where does your protein localize in the cell?
(these sites use different algorithms, so check out if they give the same result)