Protein Inference - Peptide Level

Introduction

PeptideShaker attempts to simplify the protein inference problem, i.e., the presence of shared peptides between protein sequences. It is here however possible to inspect the protein inference status of a specific peptide.

Peptides are color coded depending on whether they can be mapped to (i) a unique protein, (ii) a group of related proteins, (iii) a group of related and unrelated proteins, or (iv) a group of unrelated proteins. Note that this classification of proteins is not perfect, and a manual validation of interesting protein groups is recommended. The drop down menu at the top allows you to change the protein inference status of the selected peptide.

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.


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Retained and Other Proteins

The retained proteins is the list of proteins where this peptide can be mapped to and which were actually retained by PeptideShaker. To inspect these type the protein accession in the top right search field of PeptideShaker when in the Overview tab.

It can however also be that a peptide is mapped to a protein which was not retained by PeptideShaker. These secondary accessions are displayed in the 'Other Proteins' table.


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