Table 4 REST: Running a simulated digest

HTTP-Method

GET

URL-Pattern

Application- Root > /protein/{protein}/digest

Example URL

http://pchopper.lifesci.dundee.ac.uk/TmrcPortal/rest/properChopper/protein/akt/digest

URL-Paramters

peptideLenMin

- The minimum length of peptides to include in the results

peptideLenMax

- The maximum length of peptides to include in the results

peptideMustHaveAllResidues

- A boolean value that determines if the peptides produced from the digests should only be included if they are present within a single peptide

ignoreCleavAtPhosSite

- A boolean value that determines whether or not to ignore cleavages that occur next to a phosphorylated amino acid

usePairWiseEnzymeDigest

- A boolean value that determines whether or not to run run the simulated digest using combinations of two enzymes at a time

keyResidues

- The key amino acids in the sequence (that should be present in peptides)

exclusionChars

- The locations of amino acids that can prove to be problematic, peptides including these amino acids are filtered out

Example URL

< Application- Root > /protein/akt/digest

Example Results

< DigestResults >

< digest >

< enzyme > Proteinase K</enzyme >

< peptide >

< indexEnd > 125</indexEnd >

< sequenceHighlighted > RMNC [S] PT [S] QI</sequenceHighlighted >

< molecularWeight > 1295.44408</molecularWeight >

< percentageSolubility > 20.0</percentageSolubility >

< retentionTime > 49.6</retentionTime >

< sequence > RMNCSPTSQI</sequence >

< indexStart > 116</indexStart >

</peptide >

- < peptide >

< indexEnd > 306</indexEnd >

< sequenceHighlighted > MK [T] F</sequenceHighlighted >

< molecularWeight > 605.22843</molecularWeight >

< percentageSolubility > 50.0</percentageSolubility >

< retentionTime > 42.96</retentionTime >

< sequence > MKTF</sequence >

< indexStart > 303</indexStart >

</peptide >

... other peptides ...

</digest >

... other digests ...

< sequence >

----Actual-Sequence----

</sequence >

</DigestResults >