Tuesday, July 16, 2013

Extract phosphopeptides from Proteome Discoverer output

Have you ever wanted to just pull the phosphopeptides out of your Proteome Discoverer output data?  Well, I did.  During my second postdoc, I primarily did global quantitative (SILAC) phosphoproteomics.  In order to extract the data, my friend Dr. Trevor Glaros (Proteomics Scientist, now at USAMRIID) and a colleague at Virginia Tech developed a macro that could pull out these valuable mods.  This was a big step forward for my research, as well as a valuable lesson in my life, that sometimes it is better to know people than it is to try to do everything yourself.

Anyway, I'm going to share this valuable Excel sheet with everyone.  You can access it here:  http://orsburn-useful.bytebuckets.com/

As a side note, I found this lesson so valuable (and this formula so useful) that I had it tattooed on my leg a while back so that I'd never forget it.

1 comment:

  1. This may have been cutting edge a few generations of Excel ago but now there is a very simple solution.
    1 - highlight your data
    2 - go to the data window in the top menu. Apply filters. Little pull down menus will appear on top of each column
    3 - in the modifications column, use the drop down menu to apply filters - text filters - Contains - "Phospho"
    4 - all the data that does not contain the word phospho disappears. You can apply similar filters on any other parameter such as peptide score/confidence.

    Now the good part is that all the original data is still there, just hidden. However, if you select all the visible data, copy and paste, the information in the new spreadsheet is only those peptides that contain phosphorylation.

    I like the tattoo but these days you don't need to remember formula.