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Table 4 REST: Running a simulated digest

From: PChopper: high throughput peptide prediction for MRM/SRM transition design

Description Gets the results associated with 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 >