MRM TRANSITION ANALYSIS API

The MRM transition analysis runs an insilico analysis of all possible conflicts providing a report of the count of total conflicts found using the same engine used in the Tandem Search API. The analysis simply queries the JAEVALEN Search Engine for all possible transition combinations, reporting the total count in isospectral conflicts. Given this heuristic analysis is new, it is put to the community to develop the final method of statistical significance, or if even such a method is necessitated.

Why have an insilico fragmentation API?

Given the structure of the precalculated JAEVALEN Search, MRM contamination frequency can easily be calculated, and otherwise computationally intensive process.

USAGE

URL

./Transition/?key=<str_access_key>&pep=<str_peptide>

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
num INTEGER 1 1 2 no space, no comma
pz STRING 2 1,2,3,4 no space, no comma
fz STRING 1 1,2,3,4 no space, no comma
ion STRING yb a,b,c,y,z 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" }

EXAMPLES

Example 01

A simple example with no PTMs applied.

API Call
  http://pub.jvln.io/Transition/?key=a1b-2c3-e4f-5&pep=LVTDLTK
JSON Out
    {
      "peptide": "LVTDLTK",
      "neutral_mass": 788.46436956466,
      "ion_type": "yb",
      "ion_z": "1",
      "ion_decay": false,
      "ion_query": {
        "y1": 147.11335273691,
        "b2": 213.16030292975,
        "y2": 248.16103121141,
        "b3": 314.20798140425,
        "y3": 361.24509519236,
        "b4": 429.23492443659,
        "y4": 476.27203822469,
        "b5": 542.31898841753,
        "y5": 577.31971669919,
        "b6": 643.36666689203,
        "y6": 676.38813061585
      },
      "result_time": "1s:617ms",
      "result_data": [
        {
          "query": [
            "y1"
          ],
          "hits": "10780"
        },
        {
          "query": [
            "y1",
            "b2"
          ],
          "hits": "487"
        },
        {
          "query": [
            "y1",
            "y2"
          ],
          "hits": "777"
        },
        {
          "query": [
            "y1",
            "b3"
          ],
          "hits": "457"
        },
        {
          "query": [
            "y1",
            "y3"
          ],
          "hits": "472"
        },
        {
          "query": [
            "y1",
            "b4"
          ],
          "hits": "472"
        },
        {
          "query": [
            "y1",
            "y4"
          ],
          "hits": "457"
        },
        {
          "query": [
            "y1",
            "b5"
          ],
          "hits": "775"
        },
        {
          "query": [
            "y1",
            "y5"
          ],
          "hits": "430"
        },
        {
          "query": [
            "y1",
            "b6"
          ],
          "hits": "10775"
        },
        {
          "query": [
            "y1",
            "y6"
          ],
          "hits": "1519"
        },
        {
          "query": [
            "b2"
          ],
          "hits": "800"
        },
        {
          "query": [
            "b2",
            "y2"
          ],
          "hits": "49"
        },
        {
          "query": [
            "b2",
            "b3"
          ],
          "hits": "64"
        },
        {
          "query": [
            "b2",
            "y3"
          ],
          "hits": "48"
        },
        {
          "query": [
            "b2",
            "b4"
          ],
          "hits": "48"
        },
        {
          "query": [
            "b2",
            "y4"
          ],
          "hits": "63"
        },
        {
          "query": [
            "b2",
            "b5"
          ],
          "hits": "49"
        },
        {
          "query": [
            "b2",
            "y5"
          ],
          "hits": "716"
        },
        {
          "query": [
            "b2",
            "b6"
          ],
          "hits": "486"
        },
        {
          "query": [
            "b2",
            "y6"
          ],
          "hits": "226"
        },
        {
          "query": [
            "y2"
          ],
          "hits": "791"
        },
        {
          "query": [
            "y2",
            "b3"
          ],
          "hits": "53"
        },
        {
          "query": [
            "y2",
            "y3"
          ],
          "hits": "145"
        },
        {
          "query": [
            "y2",
            "b4"
          ],
          "hits": "145"
        },
        {
          "query": [
            "y2",
            "y4"
          ],
          "hits": "53"
        },
        {
          "query": [
            "y2",
            "b5"
          ],
          "hits": "788"
        },
        {
          "query": [
            "y2",
            "y5"
          ],
          "hits": "46"
        },
        {
          "query": [
            "y2",
            "b6"
          ],
          "hits": "777"
        },
        {
          "query": [
            "y2",
            "y6"
          ],
          "hits": "130"
        },
        {
          "query": [
            "b3"
          ],
          "hits": "751"
        },
        {
          "query": [
            "b3",
            "y3"
          ],
          "hits": "74"
        },
        {
          "query": [
            "b3",
            "b4"
          ],
          "hits": "74"
        },
        {
          "query": [
            "b3",
            "y4"
          ],
          "hits": "743"
        },
        {
          "query": [
            "b3",
            "b5"
          ],
          "hits": "53"
        },
        {
          "query": [
            "b3",
            "y5"
          ],
          "hits": "63"
        },
        {
          "query": [
            "b3",
            "b6"
          ],
          "hits": "457"
        },
        {
          "query": [
            "b3",
            "y6"
          ],
          "hits": "218"
        },
        {
          "query": [
            "y3"
          ],
          "hits": "861"
        },
        {
          "query": [
            "y3",
            "b4"
          ],
          "hits": "861"
        },
        {
          "query": [
            "y3",
            "y4"
          ],
          "hits": "74"
        },
        {
          "query": [
            "y3",
            "b5"
          ],
          "hits": "145"
        },
        {
          "query": [
            "y3",
            "y5"
          ],
          "hits": "48"
        },
        {
          "query": [
            "y3",
            "b6"
          ],
          "hits": "472"
        },
        {
          "query": [
            "y3",
            "y6"
          ],
          "hits": "135"
        },
        {
          "query": [
            "b4"
          ],
          "hits": "861"
        },
        {
          "query": [
            "b4",
            "y4"
          ],
          "hits": "74"
        },
        {
          "query": [
            "b4",
            "b5"
          ],
          "hits": "145"
        },
        {
          "query": [
            "b4",
            "y5"
          ],
          "hits": "48"
        },
        {
          "query": [
            "b4",
            "b6"
          ],
          "hits": "472"
        },
        {
          "query": [
            "b4",
            "y6"
          ],
          "hits": "135"
        },
        {
          "query": [
            "y4"
          ],
          "hits": "743"
        },
        {
          "query": [
            "y4",
            "b5"
          ],
          "hits": "53"
        },
        {
          "query": [
            "y4",
            "y5"
          ],
          "hits": "63"
        },
        {
          "query": [
            "y4",
            "b6"
          ],
          "hits": "457"
        },
        {
          "query": [
            "y4",
            "y6"
          ],
          "hits": "218"
        },
        {
          "query": [
            "b5"
          ],
          "hits": "788"
        },
        {
          "query": [
            "b5",
            "y5"
          ],
          "hits": "46"
        },
        {
          "query": [
            "b5",
            "b6"
          ],
          "hits": "775"
        },
        {
          "query": [
            "b5",
            "y6"
          ],
          "hits": "130"
        },
        {
          "query": [
            "y5"
          ],
          "hits": "716"
        },
        {
          "query": [
            "y5",
            "b6"
          ],
          "hits": "429"
        },
        {
          "query": [
            "y5",
            "y6"
          ],
          "hits": "219"
        },
        {
          "query": [
            "b6"
          ],
          "hits": "10775"
        },
        {
          "query": [
            "b6",
            "y6"
          ],
          "hits": "1518"
        },
        {
          "query": [
            "y6"
          ],
          "hits": "2583"
        }
      ]
    }