INSILICO API

This interface provides a means to calculate the insilico predicted fragmentation patterns expected for proteotypic peptides with flexible variable modifications.

Why have an insilico fragmentation API?

This creates a nice abstraction to the complicated method of calculating fragmentation patterns. In addition, it provides a method for error checking the core foundation to the TANDEM IO API.

USAGE

URL

./Insilico/?key=<str_access_key>&pep=<str_sequence>&ion=<str_fragment_types>&z=<int_charge>&decay=<str_decay>

Methods

GET or POST
Both methods are compatible with either http or https. It is recommended to use https as this encrypts your data and access token.

Request Parameters :: Summary
parameter type usage default accepted note
pep STRING required * * no spaces
ion STRING yb a,b,c,y,z no space, no comma
z STRING 12 1,2,3,4 no space, no comma
decay STRING w,a no space, no comma
Request Parameters :: Detail
Responses:
code type content
200 success see example 1
400 bad request { error : "precursor mass (pm) parameter undefined" }
401 unauthorized { error : "key not found" }
429 too many requests { error : "too many requests" }

Note: values outside of the defined accepted inputs for ion, z, and decay will fail silently


EXAMPLES

Example 01

A simple example with no PTMs applied.

API Call
  http://pub.jvln.io/Insilico/?key=a1b-2c3-e4f-5&pep=LVTDLTK
JSON Out
    {
      "peptide": "LVTDLTK",
      "neutral_mass": 788.46436956466,
      "ion_type": "yb",
      "ion_z": "12",
      "ion_decay": false,
      "result_time": "001ms",
      "result_data": {
        "y1 2+": 74.060314601895,
        "y2 2+": 124.58415383915,
        "y1": 147.11335273691,
        "y3 2+": 181.12618582962,
        "b2": 213.16030292975,
        "y4 2+": 238.63965734579,
        "y2": 248.16103121141,
        "y5 2+": 289.16349658303,
        "b3": 314.20798140425,
        "y6 2+": 338.69770354137,
        "y3": 361.24509519236,
        "b4": 429.23492443659,
        "y4": 476.27203822469,
        "b5": 542.31898841753,
        "y5": 577.31971669919,
        "b6": 643.36666689203,
        "y6": 676.38813061585
      }
    }
Example 02

Using the optional arguments.

API Call
  http://pub.jvln.io/Insilico/?key=a1b-2c3-e4f-5&pep=LVTDLTK&ion=ybc&decay=w&z=1
JSON Out
    {
      "peptide": "LVTDLTK",
      "neutral_mass": 788.46436956466,
      "ion_type": "ybc",
      "ion_z": "1",
      "ion_decay": "w",
      "result_time": "002ms",
      "result_data": {
        "y1": 147.11335273691,
        "b2-w": 195.14973824335,
        "b2": 213.16030292975,
        "y2-w": 230.15046652502,
        "c2": 230.18685203146,
        "y2": 248.16103121141,
        "b3-w": 296.19741671785,
        "b3": 314.20798140425,
        "c3": 331.23453050596,
        "y3-w": 343.23453050596,
        "y3": 361.24509519236,
        "b4-w": 411.22435975019,
        "b4": 429.23492443659,
        "c4": 446.26147353829,
        "y4-w": 458.2614735383,
        "y4": 476.27203822469,
        "b5-w": 524.30842373114,
        "b5": 542.31898841753,
        "y5-w": 559.30915201279,
        "c5": 559.34553751924,
        "y5": 577.31971669919,
        "b6-w": 625.35610220564,
        "b6": 643.36666689203,
        "y6-w": 658.37756592946,
        "c6": 660.39321599374,
        "y6": 676.38813061585
      }
    }
Example 03

Incorporating PTMs.

API Call
  http://pub.jvln.io/Insilico/?key=a1b-2c3-e4f-5&pep=LV[T79.966]DLTK
JSON Out
    {
      "peptide": "LV[T79.966]DLTK",
      "neutral_mass": 868.43036956466,
      "ion_type": "yb",
      "ion_z": "12",
      "ion_decay": false,
      "result_time": "002ms",
      "result_data": {
        "y1 2+": 74.060314601895,
        "y2 2+": 124.58415383915,
        "y1": 147.11335273691,
        "y3 2+": 181.12618582962,
        "b2": 213.16030292975,
        "y4 2+": 238.63965734578,
        "y2": 248.16103121141,
        "y5 2+": 329.14649658303,
        "y3": 361.24509519235,
        "y6 2+": 378.68070354137,
        "b3": 394.17398140425,
        "y4": 476.27203822469,
        "b4": 509.20092443658,
        "b5": 622.28498841753,
        "y5": 657.28571669919,
        "b6": 723.33266689203,
        "y6": 756.35413061585
      }
    }