This method returns the taxonomic lowest common ancestor for 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 pept2lca method can be used by doing a HTTP POST-request (preferred) or GET-request to http://api.unipept.ugent.be/api/v1/pept2lca. 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 taxonomic lowest common ancestor for 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 return the complete lineage of the taxonomic lowest common ancestor. See the response section for an overview of the information fields returned.

names

names is an optional parameter and can either be true or false. When not set explicitly, the parameter defaults to false. When both names and extra are set to true, Unipept will return the names of all ranks in the lineage of the taxonomic lowest common ancestor. Setting only names to true will not result in additional information fields being returned. See the response section for an overview of the information fields returned.

Performance penalty

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

Response

The taxonomic lowest common ancestors associated with the given peptides are returned as a list of JSON objects. By default, each object contains the following information fields extracted from the UniProt entry and NCBI taxonomy:

  • peptide: the peptide that was searched for
  • taxon_id: the NCBI taxon id of the taxonomic lowest common ancestor
  • taxon_name: the name of the taxonomic lowest common ancestor
  • taxon_rank: the taxonomic rank of the taxonomic lowest common ancestor

When the extra parameter is set to true, objects contain additional information about the lineage of the taxonomic lowest common ancestor extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields:

  • superkingdom_id
  • kingdom_id
  • subkingdom_id
  • superphylum_id
  • phylum_id
  • subphylum_id
  • superclass_id
  • class_id
  • subclass_id
  • infraclass_id
  • superorder_id
  • order_id
  • suborder_id
  • infraorder_id
  • parvorder_id
  • superfamily_id
  • family_id
  • subfamily_id
  • tribe_id
  • subtribe_id
  • genus_id
  • subgenus_id
  • species_group_id
  • species_subgroup_id
  • species_id
  • subspecies_id
  • varietas_id
  • forma_id

When both the names and extra parameter are set to true, objects also contain the names for each rank in the lineage using the following information fields:

  • superkingdom_name
  • kingdom_name
  • subkingdom_name
  • superphylum_name
  • phylum_name
  • subphylum_name
  • superclass_name
  • class_name
  • subclass_name
  • infraclass_name
  • superorder_name
  • order_name
  • suborder_name
  • infraorder_name
  • parvorder_name
  • superfamily_name
  • family_name
  • subfamily_name
  • tribe_name
  • subtribe_name
  • genus_name
  • subgenus_name
  • species_group_name
  • species_subgroup_name
  • species_name
  • subspecies_name
  • varietas_name
  • forma_name

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 lineage information fields if true.

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

Return names of ranks in the lineage if true.

Value: Must be true or false (default)

Examples

Example Retrieve the taxonomic lowest common ancestor for a given tryptic peptide

This example retrieves the taxonomic lowest common ancestor for the tryptic peptide AIPQLEVARPADAYETAEAYR. 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/pept2lca \
-d 'input[]=AIPQLEVARPADAYETAEAYR'
GET
http://api.unipept.ugent.be/api/v1/pept2lca.json?input[]=AIPQLEVARPADAYETAEAYR

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    taxon_id: 1680,
    taxon_name: 'Bifidobacterium adolescentis',
    taxon_rank: 'species'
  }
]

Example Retrieve the taxonomic lowest common ancestor for each of multiple tryptic peptides

This example retrieves the taxonomic lowest common ancestor for both the tryptic peptides AIPQLEVARPADAYETAEAYR and APVLSDSSCK. 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/pept2lca \
-d 'input[]=AIPQLEVARPADAYETAEAYR' \
-d 'input[]=APVLSDSSCK'
GET
http://api.unipept.ugent.be/api/v1/pept2lca.json?input[]=AIPQLEVARPADAYETAEAYR&input[]=APVLSDSSCK

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    taxon_id: 1680,
    taxon_name: 'Bifidobacterium adolescentis',
    taxon_rank: 'species'
  },
  {
    peptide: 'APVLSDSSCK',
    taxon_id: 9823,
    taxon_name: 'Sus scrofa',
    taxon_rank: 'species'
  }
]

Example Retrieve the taxonomic lowest common ancestor for a single tryptic peptide, while equating I and L

This example retrieves the taxonomic lowest common ancestor for the tryptic peptide APVISDSSCK. 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/pept2lca \
-d 'input[]=APVISDSSCK' \
-d 'equate_il=true'
GET
http://api.unipept.ugent.be/api/v1/pept2lca.json?input[]=APVISDSSCK&equate_il=true

Response

[
  {
    peptide: 'APVISDSSCK',
    taxon_id: 9823,
    taxon_name: 'Sus scrofa',
    taxon_rank: 'species'
  }
]

Example Retrieve the taxonomic lowest common ancestor and lineage for a single tryptic peptide

This example retrieves the taxonomic lowest common ancestor for the tryptic peptide AIPQLEVARPADAYETAEAYR including its complete lineage. 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/pept2lca \
-d 'input[]=AIPQLEVARPADAYETAEAYR' \
-d 'extra=true'
GET
http://api.unipept.ugent.be/api/v1/pept2lca.json?input[]=AIPQLEVARPADAYETAEAYR&extra=true

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    taxon_id: 1680,
    taxon_name: 'Bifidobacterium adolescentis',
    taxon_rank: 'species',
    superkingdom_id: 2,
    kingdom_id: null,
    subkingdom_id: null,
    superphylum_id: null,
    phylum_id: 201174,
    subphylum_id: null,
    superclass_id: null,
    class_id: 1760,
    subclass_id: 85003,
    infraclass_id: null,
    superorder_id: null,
    order_id: 85004,
    suborder_id: null,
    infraorder_id: null,
    parvorder_id: null,
    superfamily_id: null,
    family_id: 31953,
    subfamily_id: null,
    tribe_id: null,
    subtribe_id: null,
    genus_id: 1678,
    subgenus_id: null,
    species_group_id: null,
    species_subgroup_id: null,
    species_id: 1680,
    subspecies_id: null,
    varietas_id: null,
    forma_id: null
  }
]

Example Retrieve the taxonomic lowest common ancestor and lineage names for a single tryptic peptide

This example retrieves the taxonomic lowest common ancestor for the tryptic peptide AIPQLEVARPADAYETAEAYR including its complete lineage with names. 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/pept2lca \
-d 'input[]=AIPQLEVARPADAYETAEAYR' \
-d 'extra=true' \
-d 'names=true'
GET
http://api.unipept.ugent.be/api/v1/pept2lca.json?input[]=AIPQLEVARPADAYETAEAYR&extra=true&names=true

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    taxon_id: 1680,
    taxon_name: 'Bifidobacterium adolescentis',
    taxon_rank: 'species',
    superkingdom_id: 2,
    superkingdom_name: 'Bacteria',
    kingdom_id: null,
    kingdom_name: '',
    subkingdom_id: null,
    subkingdom_name: '',
    superphylum_id: null,
    superphylum_name: '',
    phylum_id: 201174,
    phylum_name: 'Actinobacteria',
    subphylum_id: null,
    subphylum_name: '',
    superclass_id: null,
    superclass_name: '',
    class_id: 1760,
    class_name: 'Actinobacteria',
    subclass_id: 85003,
    subclass_name: 'Actinobacteridae',
    infraclass_id: null,
    infraclass_name: '',
    superorder_id: null,
    superorder_name: '',
    order_id: 85004,
    order_name: 'Bifidobacteriales',
    suborder_id: null,
    suborder_name: '',
    infraorder_id: null,
    infraorder_name: '',
    parvorder_id: null,
    parvorder_name: '',
    superfamily_id: null,
    superfamily_name: '',
    family_id: 31953,
    family_name: 'Bifidobacteriaceae',
    subfamily_id: null,
    subfamily_name: '',
    tribe_id: null,
    tribe_name: '',
    subtribe_id: null,
    subtribe_name: '',
    genus_id: 1678,
    genus_name: 'Bifidobacterium',
    subgenus_id: null,
    subgenus_name: '',
    species_group_id: null,
    species_group_name: '',
    species_subgroup_id: null,
    species_subgroup_name: '',
    species_id: 1680,
    species_name: 'Bifidobacterium adolescentis',
    subspecies_id: null,
    subspecies_name: '',
    varietas_id: null,
    varietas_name: '',
    forma_id: null,
    forma_name: ''
  }
]

Try it

Use the API explorer form below to call the pept2lca method on live data and see the response.

Request


Response