How to change typical protein

Filtering can be done on 1 or more User Context. Once desired contexts are selected, you can

• Right-click on contexts in MSI database ans select Algorithms → Change typical protein
• Or choose MS Identification –> Context –> Algorithms → Change typical protein

The following window will appear

Typical protein modification is based on rules combinations, in the same way as in IRMa.

User should :

• specify a set of rules defining
  • a name (which will be referenced in rules compositions)
  • the field on which the rule will be applied : accession or description
  • the test operation which will be executed : starts with / ends with / contains or don't contains
  • the text to search in the given field (Case sensitive)
• specify one or more rules compositions
  • use rule name (without any other characters such as < or “) in logical composition

User wants to select as typical, protein which has

• its description starting with “sp”
• or its description starting with “tr” and its accession ending with “_HUMAN”

To do this the user will have to create 3 rules :

1. rule1 : description starts with “sp”
2. rule2 : description starts with “tr”
3. rule3 : accession ends with “_HUMAN”

and creates the following rule composition: rule1 or (rule2 and rule3 ).
When running the module, for each PutativeProtein the typical protein will be set to the first one which respects the rule composition constraint.

In this example, the user will preferentially wants to select as typical a protein which has its description starting with “sp”.
If no protein respect that constraint then user will want to select as typical a protein which has its description starting with “tr” and its accession ending with “_HUMAN”.

If we uses the same rules as in example 1 (rule1 , rule2 and rule3 ), the typical protein to choose will be one (the first) which respect rule1 and if none is found the new typical protein should respect rules composition (rule2 or rule3).
To do this, the user will have to create 3 rules :

1. rule1 : description starts with “sp”
2. rule2 : description starts with “tr”
3. rule3 : accession ends with “_HUMAN”

create two rules compositions:

1. C1 : rule1
2. C2 : rule2or rule3

and order rules compositions by priority

• C1 will be specified in prority 1 field then C2 in priority 2 field