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proteinModification(),  pmod()

The proteinModification() or pmod() function can be used only as an argument within a proteinAbundance() function to indicate modification of the specified protein. Multiple modifications can be applied to the same protein abundance. Modified protein abundance term expressions have the general form:

p(ns:protein_value, pmod(ns:type_value, <code>, <pos>))

type_value (required) is a namespace value for the type of modification , <code> (optional) is a single-letter or three-letter code for one of the twenty standard amino acids, and <pos> (optional) is the position at which the modification occurs based on the reference sequence for the protein. If <pos> is omitted, then the position of the modification is unspecified. If both <code> and <pos> are omitted, then the residue and position of the modification are unspecified. NOTE - A default BEL namespace includes commonly used protein modification types.

Examples

AKT1 phosphorylated at Serine 473

default BEL namespace and 1-letter amino acid code:

p(HGNC:AKT1, pmod(Ph, S, 473))

 

default BEL namespace and 3-letter amino acid code:

p(HGNC:AKT1, pmod(Ph, Ser, 473))

 

PSI-MOD namespace and 3-letter amino acid code:

p(HGNC:AKT1, pmod(MOD:PhosRes, Ser, 473))
MAPK1 phosphorylated at both Threonine 185 and Tyrosine 187

default BEL namespace and 3-letter amino acid code:

p(HGNC:MAPK1, pmod(Ph, Thr, 185), pmod(Ph, Tyr, 187))
Palmitoylated HRAS

HRAS palmitoylated at an unspecified residue. Default BEL namespace:

p(HGNC:HRAS, pmod(Palm))

 

 
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