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fragment(), frag()

The fragment() or frag() function can be used within a proteinAbundance() term to specify a protein fragment, e.g., a product of proteolytic cleavage. Protein fragment expressions take the general form:

p(ns:v, frag(<range>, <descriptor>))

where <range> (required) is an amino acid range, and <descriptor> (optional) is any additional distinguishing information like fragment size or name.


For these examples, HGNC:YFG is ‘your favorite gene’. For the first four examples, only the <range> argument is used. The last examples include use of the optional <descriptor>.

fragment with known start/stop
p(HGNC:YFG, frag(5_20))
amino-terminal fragment of unknown length
p(HGNC:YFG, frag(1_?))
carboxyl-terminal fragment of unknown length
p(HGNC:YFG, frag(?_*))
fragment with unknown start/stop
p(HGNC:YFG, frag(?))
fragment with unknown start/stop and a descriptor
p(HGNC:YFG, frag(?, 55kD))
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