With Mascot Server 1.9 and later, all peptide mass fingerprint searches test for the possibility that the sample is a mixture of proteins. Mascot will automatically detect and report statistically significant protein mixtures of up to six components. The results are saved in a 'mixtures' section of the results file. The 'summary' section of the results file is unchanged.
ms_proteinsummary::getHit() can return a protein that is a 'mixture'. However, this is not a 'real' protein but just a container for a number of component proteins. To determine if the protein is a 'mixture', use the method ms_protein::isPMFMixture().
This 'mixture protein' has a list of peptides and in general can be treated as a normal protein object, with the difference that its accession will be "Mixture k", where k is an integer. Also, the description line returned from ms_mascotresults::getProteinDescription() will be of the form:
Mixture from proteins:"gi|1234","gi|5432","gi|9999"
ms_mascotresults::getProteinMass() will always be zero for 'mixtures'.
To find the number of peptides that matched, use ms_protein::getNumDisplayPeptides(). Only peptides that matched in two or more component proteins are counted in the number. To display a 'colour coded' report, the component ID for the
getComponent() call is also available for each peptide that matched with ms_protein::getProteinComponentID().
For the concise protein summary report, a single protein is never collapsed into a mixture and a mixture is never collapsed into a single protein.
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