Saturday, December 14, 2013

Spectral counting in Proteome Discoverer

The image above is stolen directly by/from Google Images.  First thing that pops up if you look up "spectral counting".  Anyway, I often get questions about using Proteome Discoverer for spectral counting.  I have some slides that I cut from an iORBI I attended several years ago showing spectral counting in PD and this is what I send people.

I'm not a big fan of spectral counting, but it does have its place sometimes.  The slides show you a comparison of spectral counting vs. quan of peaks at the MS1 intensity level as the limitations in dynamic range from spectral counting (with a very nice reference).

EDIT (2/1/17) New DropBox link!


  1. Hi Ben. All files stored in bytebuckets are down. Have you transferred them elsewhere? Thanks!

    1. Oh no! Yeah...I need to update these links, sorry!