H. Lee Moffitt Cancer Center & Research Institute

pY Index & Count


pY Index&Count process the export Excel files from Scaffold and calculate the phosphorylated Tyrosine(Y) index position and the total number of appearance.


pY Index&Count is deployed as an Add-in of Microsoft Excel application. This add-in will add a new menu to Excel as the following figure shows:

The new menu is called “Proteome” and it currently has three menu items:

  • Phospho Y Index & Count
  • Combine Count
  • About
The first menu item – Phospho Y Index & Count – is used to generate a report from the spectrum report exported from Scaffold. The phosphor Y index and count report contains the phospho Y index in proteins for all the peptides; it also contains the number of appearance of such phospho Y in a particular protein for all the identified peptides.

The second menu item – Combine Count – is used to combine the counts for peptides of the following form:

That is, one peptide is a substring of another peptide.


Please see the Installation Guide for detail information.


Please see the User Guide for detail information.


© Copyright 2008 Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute