Protein Inference

Inferring proteins from peptides is not as simple as it may seem. Some peptides can map to multiple proteins, for example Protein A and Protein B. If no unique peptide ensures the presence of A or B, PeptideShaker cannot say whether Protein A or Protein B (or both) is present.

The PI column in the Overview tab stands for Protein Inference. Proteins are here flagged depending on the type of protein inference:

For each type PeptideShaker provides a set of options so that one can manually select the protein consider as the correct one.

In many cases the protein groups are closely related proteins like isoforms and depending on your experiment distinguishing between these may or may not be important.

To support your decision you have the list of Unique Hits (if any) of each possible protein, and the list of Related Hits (if any) to this group.

For proteins from UniProt you also have the protein evidence to guide the selection. For more information about protein evidence see:
http://www.uniprot.org/manual/protein_existence.

To change the protein inference group for the currently selected protein, select the wanted protein in the Candidate Proteins table and click OK. The selection will be automatically updated in the rest of PeptideShaker.

For an introduction to protein inference see:
Nesvizhskii et al: Interpretation of shotgun proteomic data: the protein inference problem, Mol Cell Proteomics. 2005 Oct;4(10):1419-40.