What is the Protein Grouping Algorithm used in Scaffold and where is it shown?
Scaffold uses a protein grouping algorithm to reduce the number of proteins under consideration. Generally, this algorithm works by creating a table like that shown in the Similarity View of Scaffold. This table shows each protein to which the peptides could potentially be assigned, and in that protein’s column shows the probabilities of all of the peptides that match it. The sum of the probabilities is calculated for each protein. Only the “valid” peptides are considered. Each peptide is then assigned to the protein with the highest total probability in whose column it appears. If two or more proteins have equal total probabilities and that is the highest for that peptide, it is assigned to all of them. Now the grouping begins. Proteins with no peptides assigned are eliminated from consideration, as all of the evidence for those proteins has already been accounted for in proteins which are more likely. Proteins with the same peptides assigned to them are combined into a group. There i
