API Reference

Details of all available Pep-Calc API resources are listed below. All URLs are relative to http://api.pep-calc.com. Query parameters should be formatted as described on the Peptide Calculator and Peptoid Calculator help pages.

Further information about the methods used in calculations carried out by Pep-Calc API is also given on the help pages and the relevant article published in the Journal of Computer-Aided Molecular Design.

Basic Properties

GET /peptide
GET /peptoid

Returns basic calculated properties for the sequence, including formula and molecularWeight. See Getting Started for an example output.

Query Parameters:
 
  • seq – peptide/peptoid sequence string
  • N_term – N-terminus chemical formula string
  • C_term – C-terminus chemical formula string

Mass Assignment

GET /peptide/mass
GET /peptoid/mass

Returns an assignment of MS peaks passed in the mz query parameter. See Further Calculation Functions for an example output.

Query Parameters:
 
  • seq – peptide/peptoid sequence string
  • N_term – N-terminus chemical formula string
  • C_term – C-terminus chemical formula string
  • mz – comma-separated list of MS peaks for assignment

Ion Series

GET /peptide/ionseries
GET /peptoid/ionseries

Returns m/z values corresponding to the series of singly- and multiply-protonated ions calculated for both the target peptide and possible single deletions/adducts. MS peaks for assignment can optionally be passed in the mz query parameter.

The top level array contains objects corresponding to deletion/adduct or molecular ion species. For each object the boolean molecular indicates whether or not the species is a molecular ion, and the arrays dels and mods describe applicable deletions and adducts respectively. The array ions contains the series of objects corresponding to calculated m/z values for the species.

For each ion the calculated m/z value (mz) and charge state (z) are provided. The boolean assigned indicates whether any MS peaks provided have been assigned to this m/z value.

Query Parameters:
 
  • seq – peptide/peptoid sequence string
  • N_term – N-terminus chemical formula string
  • C_term – C-terminus chemical formula string
  • mz – (optional) comma-separated list of MS peaks for assignment

Isoelectric Point

GET /peptide/iso

Returns a calculated isoelectric point (pI) for the peptide sequence. A null value will be returned for sequences with nonexistent or out of range isoelectric points.

See the Basic Properties resource for required query parameters.

Charge Summary

GET /peptide/charges

Returns totals of acidic (acidicCount), basic (basicCount), uncharged (unchargedCount) and unclassified/nonstandard (otherCount) residues for the peptide sequence.

See the Basic Properties resource for required query parameters.

Extinction Coefficient

GET /peptide/extinction

Returns calculated molar extinction coefficient values for the peptide sequence, based on either the maximum number of disulfide bonds possible (oxidized) or the absence of disulfides (reduced).

Query Parameters:
 
  • seq – peptide sequence string

ChemDraw Generation

GET /peptide/chemdraw
GET /peptoid/chemdraw

Returns a ChemDraw file generated for the sequence in .cdxml format.

See the Basic Properties resource for required query parameters.

Beta Contiguity

GET /peptide/betacontiguity

Returns an array of \beta-strand propensity values for the peptide sequence, ordered by residue number. See Beta Contiguity Calculation for an example output. A null value will be returned for sequences not containing any predicted beta-strand forming regions.

See the Basic Properties resource for required query parameters.