fragment [frag] v.2.1.0 (current)

Long form: fragment() Short form: 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(, ))

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

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

Function Signatures

fragment(StrArg, StrArg)

  1. String argument of following type(s): /[\d_\?*]+/

  2. String argument of following type(s): /.*?/

Examples

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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