#FRAMEWORK PROTEIN SCAFFOLD PLUS#

As in the case of the Legacy Protein Grouping, the Shared peptide Grouping algorithm thins down the list of proteins by eliminating any for which there is no independent evidence. Next, the protein list is pared down according to the principle of parsimony. These weights are also displayed in the Proteins View Peptide table in the column titled 'Apportionments' which replaces the traditional 'Assigned' column when the cluster grouping model is used. The Scaffold default cutoff is 0%.Īs an example, Figure 4 shows the peptides shared by multiple proteins with their related weights listed in the Similarity view.įigure 4. A peptide can be set 'valid' either manually, by unchecking peptides in the Proteins View Peptide table or globally by using the Experiment menu option Reset Peptide Validation. This value is normalized by the sum of the exclusive peptide evidence for each of the proteins that contain peptide p. PE excl(A), the exclusive peptide evidence is defined as the sum of the probabilities of each exclusive unique valid peptide X belonging to protein A. Where W(p,a) is the weight assigned to shared peptide p contained in protein A and in other proteins. The weights are assigned using the following formula: Samples table, protein groupingįor the purpose of calculating the protein probabilities, shared peptides are apportioned among proteins according the a weighting function. The 'preferred' or named protein is selected arbitrarily and may be changed by the user.įigure 3.

#FRAMEWORK PROTEIN SCAFFOLD PLUS#

These proteins appear in the Samples Table as a single line with the accession number of one of them followed by a plus sign and the number of other proteins in the group. In cases where two or more proteins share all of their peptides, there is no basis for discrimination among them and the proteins are treated as a unit called a protein group. Scaffold considers proteins that share peptide evidence. It then proceeds to form 'Protein Groups' and assign weights to each shared peptide, see Weighting Function. Rather than assigning each peptide to a single protein, Shared Peptide Grouping includes a peptide in all of its matching proteins.

The way shared Peptide Grouping assigns peptides to proteins is quite different from how it is done in the Legacy Peptide Grouping algorithm. Selecting the box for Protein Cluster Analysis and clicking Apply creates clusters using Shared Peptide Grouping and Protein Cluster Analysis.įor explanatory purposes, the grouping and clustering processes can be broken down into the following three phases: Note, this menu option is only found in a fully licensed version of Scaffold, not in a viewer. If during file loading, Protein Cluster Analysis is not selected, it can be reapplied to the already loaded data by going to the Experiment > Edit Experiment. Choosing this option enables the application of both Shared Peptide Grouping and Protein Cluster Analysis. The protein grouping option is selected during file loading by checking Use Protein Cluster Analysis in the Load and Analyze page of Scaffold's Load data Wizard. Scaffold also includes the option to assemble proteins into clusters based on shared peptide evidence using Protein Cluster Analysis. Shared Peptide Grouping is designed to lessen the probability of discarding a valid protein identification when the proteins happens to share peptides with another identified protein. Previous versions of Scaffold, prior to version 4, instead used a different grouping algorithm referred to as the Legacy Protein Grouping.

Scaffold includes the option of applying a method of grouping proteins called Shared Peptide Grouping. Shared Peptide Grouping and Protein Cluster Analysis Displaying Clusters in the Samples Table- an Example.Clustering Algorithm at Work- an Example.Shared Peptide Grouping and Protein Cluster Analysis.The grouping and paring is achieved using different algorithms depending on whether the Protein Cluster Analysis is selected or not. The following document describes the way Scaffold groups and thins out the list of proteins shown in the Samples table so the user can focus on the most likely protein identifications present in the experiment.

Framework protein scaffold