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Protein grouping is done from a parent context and consist of
Peptides from different child context or identifications - attached directly or indirectly to a context - are grouped.
Peptides must have same sequence and same experimental mass to be grouped.
Peptide grouping results in new peptides attached to the parent context and having child peptides
A new peptide is construct as follow :
charge, sequence, ptm, missed cleavage and calculated mass
are copied from the first child peptide found experimental mass and retention time
are set to childs averagescore
is set to the max of child scoreschild list
is set as peptides with same sequence, same mass are foundmatches list
associated to new peptide, matches from all child peptides are grouped using matched protein. Created match score
is set to the max of all child matches scores and start and end
value are equal to child matches start and end.Different filters could be applied during grouping.
new matches
are created. new matches
are created. Typically this correspond to filter protein with less than x peptides…
The filtered protein or species are not taken into account in the final grouping result, they are removed from result (unlike during protein filter (:: add link)). An other difference with protein filter
operation is that filtering is done on each proteins.
Once new peptides have been created and associated to parent context, same grouping as done by Mascot® and IRMa is done.
But before executing the protein grouping the list of proteins to be considered is filtered using optional protein filter. This means that proteins are filtered individually and filter is not applied to protein group level. See protein group filters page.
Protein grouping consist in :
Protein grouping results in new groups of proteins and peptides, attached to the parent context. The protein group and proteins matching properties are set as follow :
You need to be carefull when grouping proteins within a tree of contexts. Let's take the following example:
Rootnode |_ Context1 |_ F085255.dat |_ F085256.dat |_ F085257.dat |_ Context2 |_ F085258.dat |_ F085259.dat
It's possible:
Rootnode
level, hEIDI will then group proteins from all the identification results, orContext1
and Context2
), then ending with the Rootnode
.
At present, when launching the protein group algorithm, you can tell hEIDI to filter some proteins and/or peptides. For example, if you decide to filter proteins with a number of peptides lower than 2, it is important to understand that doing this may give different results in cases 1 & 2.
Rootnode |_ Context1 ProtA (pep1, pep2) |_ Context2 ProtA (pep1, pep5)
In case 2, ProtA will be filtered at an early stage (when grouping proteins in Context1
and Context2
), and will not appear in the final result.
But in case 1, when grouping proteins at the Rootnode
level, ProtA will 'gain' one peptide more (ProtA will be identified by 3 peptides instead of 2). So, ProtA will not be filtered and will appear in the final result.