This method returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.

Request

The pept2funct method can be used by doing a HTTP POST-request (preferred) or GET-request to http://api.unipept.ugent.be/api/v1/pept2go. Parameters can be included in the request body (POST) or in the query string (GET). The only required parameter is input[], which takes one or more tryptic peptides.

input

input[] is a required parameter that takes one or more tryptic peptides. Unipept will return the functional EC-numbers and GO-terms associated with each of the input[] peptides based on their occurence in UniProt entries. To pass multiple peptides at once, simply add multiple input[] parameters (see example).

Input size

Unipept puts no restrictions on the number of peptides passed to the input[] parameter. Keep in mind that searching for lots of peptides at once may cause the request to timeout or, in the case of a GET-request, exceed the maximum URL length. When performing bulk searches, we suggest splitting the input set over requests of 100 peptides each.

equate_il

equate_il is an optional parameter and can either be true or false. When not set explicitly, the parameter defaults to false. When the parameter is set to true, isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt entries. This setting is similar to checking the Equate I and L? checkbox when performing a search with the Tryptic Peptide Analysis in the web interface.

extra

extra is an optional parameter and can either be true or false. When not set explicitly, the parameter defaults to false. When the parameter is set to true, Unipept will also return the name associated with a GO-term and an EC-number. See the response section for an overview of the information fields returned.

split

split is an optional parameter that can be used to order the GO-terms in groups according to their namespace (cellular component, molecular function, biological process).

Performance penalty

Setting extra or split to true has a performance penalty inferred from additional database queries. Do not use this parameter unless the extra information fields are needed.

Response

A list of JSON objects is returned. By default, each object contains the following information fields:

  • peptide: The peptide that was searched for.
  • total_protein_count: Total amount of proteins matched with the given peptide.
  • ec: A list of JSON objects that each represent an EC-number associated with the current tryptic peptide.
    • ec_number: The EC-number associated with the current tryptic peptide.
    • protein_count: The amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
    • name: Optional, name of the EC-number. Included when the extra parameter is set to true.
  • go: A list of JSON objects that each represent a GO-term associated with the current tryptic peptide.
    • go_term: The GO-term associated with the current tryptic peptide.
    • protein_count: The amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
    • name: Optional, name of the GO-term. Included when the extra parameter is set to true.

When the split parameter is set to true, objects are placed in a group corresponding to their namespace and the objects are nested in an additional object. See the examples for more information.

Parameters

Name Description
input[]
required

Tryptic peptide to search for. Add multiple parameters to search for multiple peptides.

Value: String
equate_il
optional

Equate isoleucine (I) and leucine (L).

Value: Must be true or false (default)
extra
optional

Return additional information fields if true.

Value: Must be true or false (default)
split
optional

Separates GO-namespaces and places objects in group associated with current namespace when true.

Value: Must be true or false (default)

Examples

Example Retrieve the functional ec-numbers and go-terms associated with a given tryptic peptide

This example retrieves all functional ec-numbers and go-terms associated with the tryptic peptide AAAAA. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2funct \
-d 'input[]=AAAAA'
GET
http://api.unipept.ugent.be/api/v1/pept2funct.json?input[]=AAAAA

Response

[
    {
        'peptide': 'AAAAA',
        'total_protein_count': 17,
        'ec': [
            {
                'ec_number': '1.5.1.5',
                'protein_count': 14
            },
            {
                'ec_number': '3.5.4.9',
                'protein_count': 14
            },
            {
                'ec_number': '2.4.1.21',
                'protein_count': 1
            }
        ],
        'go': [
            {
                'go_term': 'GO:0006164',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0004488',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0035999',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0009086',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0000105',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0004477',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0003677',
                'protein_count': 2
            },
            {
                'go_term': 'GO:0016987',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0044219',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009011',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005198',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009399',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005525',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0003723',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0046740',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0019028',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0004373',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0006352',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0001216',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005978',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0003899',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0033201',
                'protein_count': 1
            }
        ]
    }
]

Example Retrieve the functional ec-numbers and go-terms associated with each of multiple tryptic peptides

This example retrieves the functional ec-numbers and go-terms for both the tryptic peptides AAAAA and AAAYGMR. The result is the same as the combination of this search and this search with the Tryptic Peptide Analysis in the web interface.

POST
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2funct \
-d 'input[]=AAAAA' \
-d 'input[]=AAAYGMR'
GET
http://api.unipept.ugent.be/api/v1/pept2funct.json?input[]=AAAAA&input[]=AAAYGMR

Response

[
    {
        'peptide': 'AAAAA',
        'total_protein_count': 17,
        'ec': [
            {
                'ec_number': '1.5.1.5',
                'protein_count': 14
            },
            {
                'ec_number': '3.5.4.9',
                'protein_count': 14
            },
            {
                'ec_number': '2.4.1.21',
                'protein_count': 1
            }
        ],
        'go': [
            {
                'go_term': 'GO:0006164',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0004488',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0035999',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0009086',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0000105',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0004477',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0003677',
                'protein_count': 2
            },
            {
                'go_term': 'GO:0016987',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0044219',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009011',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005198',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009399',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005525',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0003723',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0046740',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0019028',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0004373',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0006352',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0001216',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005978',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0003899',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0033201',
                'protein_count': 1
            }
        ]
    },
    {
        'peptide': 'AAAYGMR',
        'total_protein_count': 2,
        'ec': [
            {
                'ec_number': '3.5.1.5',
                'protein_count': 1
            }
        ],
        'go': [
            {
                'go_term': 'GO:0005737',
                'protein_count': 2
            },
            {
                'go_term': 'GO:0005886',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0006605',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005524',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0043419',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0016151',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0017038',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009039',
                'protein_count': 1
            }
        ]
    }
]

Example Retrieve the functional ec-numbers and go-terms associated with a single tryptic peptide, while equating I and L

This example retrieves the functional ec-numbers and go-terms associated with the tryptic peptide AAAAA. In searching, isoleucine (I) and leucinge (L) are considered equal. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2funct \
-d 'input[]=AAAAA' \
-d 'equate_il=true'
GET
http://api.unipept.ugent.be/api/v1/pept2funct.json?input[]=AAAAA&equate_il=true

Response

[
    {
        'peptide': 'AAAAA',
        'total_protein_count': 17,
        'ec': [
            {
                'ec_number': '1.5.1.5',
                'protein_count': 14
            },
            {
                'ec_number': '3.5.4.9',
                'protein_count': 14
            },
            {
                'ec_number': '2.4.1.21',
                'protein_count': 1
            }
        ],
        'go': [
            {
                'go_term': 'GO:0006164',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0004488',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0035999',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0009086',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0000105',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0004477',
                'protein_count': 14
            },
            {
                'go_term': 'GO:0003677',
                'protein_count': 2
            },
            {
                'go_term': 'GO:0016987',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0044219',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009011',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005198',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0009399',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005525',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0003723',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0046740',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0019028',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0004373',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0006352',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0001216',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0005978',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0003899',
                'protein_count': 1
            },
            {
                'go_term': 'GO:0033201',
                'protein_count': 1
            }
        ]
    }
]

Example Retrieve the functional ec-numbers and go-terms associated with a single tryptic peptide, with extra information enabled

This example retrieves the functional ec-numbers and go-terms associated with the tryptic peptide AAAAA including the name of each ec-number and go-term. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2funct \
-d 'input[]=AAAAA' \
-d 'extra=true'
GET
http://api.unipept.ugent.be/api/v1/pept2funct.json?input[]=AAAAA&extra=true

Response

[
    {
        'peptide': 'AAAAA',
        'total_protein_count': 17,
        'ec': [
            {
                'ec_number': '1.5.1.5',
                'protein_count': 14,
                'name': 'Methylenetetrahydrofolate dehydrogenase (NADP(+))'
            },
            {
                'ec_number': '3.5.4.9',
                'protein_count': 14,
                'name': 'Methenyltetrahydrofolate cyclohydrolase'
            },
            {
                'ec_number': '2.4.1.21',
                'protein_count': 1,
                'name': 'Starch synthase'
            }
        ],
        'go': [
            {
                'go_term': 'GO:0006164',
                'protein_count': 14,
                'name': 'purine nucleotide biosynthetic process'
            },
            {
                'go_term': 'GO:0004488',
                'protein_count': 14,
                'name': 'methylenetetrahydrofolate dehydrogenase (NADP+) activity'
            },
            {
                'go_term': 'GO:0035999',
                'protein_count': 14,
                'name': 'tetrahydrofolate interconversion'
            },
            {
                'go_term': 'GO:0009086',
                'protein_count': 14,
                'name': 'methionine biosynthetic process'
            },
            {
                'go_term': 'GO:0000105',
                'protein_count': 14,
                'name': 'histidine biosynthetic process'
            },
            {
                'go_term': 'GO:0004477',
                'protein_count': 14,
                'name': 'methenyltetrahydrofolate cyclohydrolase activity'
            },
            {
                'go_term': 'GO:0003677',
                'protein_count': 2,
                'name': 'DNA binding'
            },
            {
                'go_term': 'GO:0016987',
                'protein_count': 1,
                'name': 'sigma factor activity'
            },
            {
                'go_term': 'GO:0044219',
                'protein_count': 1,
                'name': 'host cell plasmodesma'
            },
            {
                'go_term': 'GO:0009011',
                'protein_count': 1,
                'name': 'starch synthase activity'
            },
            {
                'go_term': 'GO:0005198',
                'protein_count': 1,
                'name': 'structural molecule activity'
            },
            {
                'go_term': 'GO:0009399',
                'protein_count': 1,
                'name': 'nitrogen fixation'
            },
            {
                'go_term': 'GO:0005525',
                'protein_count': 1,
                'name': 'GTP binding'
            },
            {
                'go_term': 'GO:0003723',
                'protein_count': 1,
                'name': 'RNA binding'
            },
            {
                'go_term': 'GO:0046740',
                'protein_count': 1,
                'name': 'transport of virus in host, cell to cell'
            },
            {
                'go_term': 'GO:0019028',
                'protein_count': 1,
                'name': 'viral capsid'
            },
            {
                'go_term': 'GO:0004373',
                'protein_count': 1,
                'name': 'glycogen (starch) synthase activity'
            },
            {
                'go_term': 'GO:0006352',
                'protein_count': 1,
                'name': 'DNA-templated transcription, initiation'
            },
            {
                'go_term': 'GO:0001216',
                'protein_count': 1,
                'name': 'bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding'
            },
            {
                'go_term': 'GO:0005978',
                'protein_count': 1,
                'name': 'glycogen biosynthetic process'
            },
            {
                'go_term': 'GO:0003899',
                'protein_count': 1,
                'name': 'DNA-directed 5'-3' RNA polymerase activity'
            },
            {
                'go_term': 'GO:0033201',
                'protein_count': 1,
                'name': 'alpha-1,4-glucan synthase activity'
            }
        ]
    }
]

Example Retrieve the functional ec-numbers and go-terms associated with a single tryptic peptide, making a distinction between different go-domains

This example retrieves the functional ec-numbers and go-terms associated with the tryptic peptide AAAAA distributed over the distinct go-domains. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2funct \
-d 'input[]=AAAAA' \
-d 'domains=true'
GET
http://api.unipept.ugent.be/api/v1/pept2funct.json?input[]=AAAAA&domains=true

Response

[
    {
        'peptide': 'AAAAA',
        'total_protein_count': 17,
        'ec': [
            {
                'ec_number': '1.5.1.5',
                'protein_count': 14
            },
            {
                'ec_number': '3.5.4.9',
                'protein_count': 14
            },
            {
                'ec_number': '2.4.1.21',
                'protein_count': 1
            }
        ],
        'go': [
            {
                'molecular function': [
                    {
                        'go_term': 'GO:0004488',
                        'protein_count': 14
                    },
                    {
                        'go_term': 'GO:0004477',
                        'protein_count': 14
                    },
                    {
                        'go_term': 'GO:0003677',
                        'protein_count': 2
                    },
                    {
                        'go_term': 'GO:0016987',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0009011',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0005198',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0005525',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0003723',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0004373',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0001216',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0003899',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0033201',
                        'protein_count': 1
                    }
                ]
            },
            {
                'cellular component': [
                    {
                        'go_term': 'GO:0044219',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0019028',
                        'protein_count': 1
                    }
                ]
            },
            {
                'biological process': [
                    {
                        'go_term': 'GO:0006164',
                        'protein_count': 14
                    },
                    {
                        'go_term': 'GO:0035999',
                        'protein_count': 14
                    },
                    {
                        'go_term': 'GO:0009086',
                        'protein_count': 14
                    },
                    {
                        'go_term': 'GO:0000105',
                        'protein_count': 14
                    },
                    {
                        'go_term': 'GO:0009399',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0046740',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0006352',
                        'protein_count': 1
                    },
                    {
                        'go_term': 'GO:0005978',
                        'protein_count': 1
                    }
                ]
            }
        ]
    }
]

Try it

Use the API explorer form below to call the pept2funct method on live data and see the response.

Request


Response