Group1 - Group2.xls = Output file containing hits present in Group 1, but not in Group 2.

Group1 n Group2.xls = Output file containing Intersection of Group 1 and Group 2

Score = Mascot Score

emPAI = Exponentially Modified Protein Abundance Index (http://www.matrixscience.com/help/quant_empai_help.html)

Coverage = Percent Coverage

Input File = File in which the given hit was identified.

*  in the column F = 3-5 fold ratio of the Mascot Scores in Group1 vs. Group2 (for operation Group1-Group2).
** in the column F = >5 fold ratio of the Mascot Scores in Group1 vs. Group2 (for operation Group1-Group2).
Note that if the ratio of the Mascot Scores between the subtracted groups is <3, the hit will be subtracted.

** in the Coverage column = An alternative method of % coverage calculation was used due to variable sequence information in the database.