MaCPepDB - Mass Centric Peptide Database

Proteins

Lookup by accession

url

http://localhost/api/proteins/<ACCESSION>

ouput

{
    "accession": "P04637",
    "entry_name": "P53_HUMAN",
    "is_reviewed": true,
    "name": "Tumor suppressor p53",
    "proteome_id": "UP000005640",
    "sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD",
    "taxonomy_id": 9606,
    "taxonomy_name": "Homo sapiens"
}

Get peptides of protein

url

http://localhost/api/proteins/<string:accession>/peptides

additional headers

Accept: application/json or text/csv (This controls the output, see below. application/json is the default and is used for unknown accept-formats)

output (application/json)

{
    "peptides": [
        {
        "is_swiss_prot": true,
        "is_trembl": true,
        "mass": 588.286739698,
        "number_of_missed_cleavages": 0,
        "proteome_ids": ["UP000186942", ...],
        "sequence": "DAQAGK",
        "taxonomy_ids": [9749, ...],
        "unique_taxonomy_ids": [9534, ...]
        },
        ...
    ]
}

output (text/csv)

mass,sequence,number_of_missed_cleavages,in_swiss_prot,in_trembl,taxonomy_ids,unique_for_taxonomy_ids,proteome_ids
588.286739698,"DAQAGK",0,"true","true","9749,9534,...","UP000186942,UP000243499,UP000037951,..."
...

Digest protein

url

http://localhost/api/proteins/digest

method

POST

additional headers

Content-Type: application/json

body (JSON)

keys:

accession: string
maximum_number_of_missed_cleavages: unsigned int
minimum_peptide_length: unsigned int
maximum_peptide_length: unsigned int

ouput

{
    "peptides": [
        {
            "mass": 588.286739698,
            "sequence": "DAQAGK",
            "length": 6,
            "number_of_missed_cleavages": 0,
            "metadata": null
        },
        ...
    ],
    count: 101
}

Get amino acids

url

http://localhost/api/proteins/amino-acids

ouput

    "amino_acids": [
        {
        "name": "Alanine",
        "one_letter_code": "A"
        },
        ...
    ]
}

There are also ambigous amino acids present!

Peptides

Lookup by sequence

url

http://localhost/api/peptides/<SEQUENCE>

Query parameter

is_reviewed: int, option, filter for SwissProt (!=0), TrEMBL (==0) and both (not present)

ouput

{
    "mass": 950.537157588,
    "sequence": "VRAMAIYK",
    "length": 8,
    "number_of_missed_cleavages": 1,
    "metadata": {
        "is_swiss_prot": true,
        "is_trembl": true,
        "taxonomy_ids": [34862, ...],
        "unique_taxonomy_ids": [34862, ...],
        "proteome_ids": ["UP000326062", ...]
    }
}

Get proteins of peptide

url

http://localhost/api/peptides/<SEQUENCE>/proteins

ouput

{
    "reviewed_proteins": [
        {
        "accession": "P41685",
        "entry_name": "P41685",
        "name": "Tumor suppressor p53",
        "sequence": "MQEPPLELTIEPPLSQETFSELWNLLPENNVLSSELSSAMNELPLSEDVANWLDEAPDDASGMSAVPAPAAPAPATPAPAISWPLSSFVPSQKTYPGAYGFHLGFLQSGTAKSVTCTYSPPLNKLFCQLAKTCPVQLWVRSPPPPGTCVRAMAIYKKSEFMTEVVRRCPHHERCPDSSDGLAPPQHLIRVEGNLHAKYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPIITIITLEDSNGKLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCPEPPPGSTKRALPPSTSSTPPQKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQSGKEPGGSRAHSSHLKAKKGQSTSRHKKPMLKREGLDSD",
        "taxonomy_id": 9685,
        "proteome_id": "UP000011712",
        "is_reviewed": true
        },
        ...
    ],
    "unreviewed_proteins_rows": [
        {
        "accession": "A4GW67",
        "entry_name": "A4GW67",
        "name": "Tumor protein p53",
        "sequence": "VGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKR",
        "taxonomy_id": 9606,
        "proteome_id": "None",
        "is_reviewed": false
        },
        ...
    ]
}

Check multiple sequences for existence

url

http://localhost/api/peptides/lookup

method

POST

body (JSON)

{
    "sequences": [
        "peptide_sequence_1",
        "peptide_sequence_2",
        "peptide_sequence_3",
        ...
    ]
}

ouput (text/plain)

peptide_sequence_1
peptide_sequence_3
...

More output formats coming soon.

Search by mass

url

http://localhost/api/peptides/search
or http://localhost/api/peptides/search.(json|stream|txt|csv)

method

POST

additional headers

Content-Type: application/json
Accept: application/json, application/octet-stream, text/plain or text/csv (This controlls the output, see below. application/json is the default and is used for unknown accept-formats)

body (JSON)

keys:

precursor: float
lower_precursor_tolerance_ppm: unsigned int
upper_precursor_tolerance_ppm: unsigned int
variable_modification_maximum: unsigned int
modifications: array of modifications, each modification is a dictionary with keys
- amino_acid: string containing the amino acid one letter code
- position: string (anywhere|n_terminus|c_terminus)
- is_static: bool, marks modification as static or variable
- delta: float, the mass change which is applied by this modification
limit: unsigned int (optional)
offset: unsigned int (optional)
taxonomy_id: unsigned int (Uniprot Taxonomy Identifier)
proteome_id: string (Uniprot Proteome Identifier: UP...)
is_reviewed: bool, default: not set, optional (selects from which database the peptides will be from, not set: Swiss-Prot + TrEMBL, true: SwissProt, false: TrEMBL)
include_count: bool, default: false, optional (includes the peptides count without limit or offset. setting this to false cut the response time by 50%, only accounted for application/json-output)
order_by: string, default: mass, optional (ignored for text/plain-output), possible values: mass length number_of_missed_cleavages sequence, default: mass,
order_direction: bool, must be present when order_by is set, possible values: asc & desc
include_metadata: bool, default: false, optional

If taxonomy_id, proteome_id, is_reviewed are used together they will concanted with and.

body (Form)

The search parameter can also be submitted as content type application/x-www-form-urlencoded. In this case provide the parameters as JSON-string in a form parameter called search_params.

output format

The output format can also be changed by prepanding a file extension

file extension	output format
`json`	`application/json`
`stream`	`application/octet-stream`
`txt`	`text/plain`
`csv`	`text/csv`

example:

{
    "precursor": 859.49506802369,
    "lower_precursor_tolerance_ppm": 5,
    "upper_precursor_tolerance_ppm": 5,
    "variable_modification_maximum": 0,
    "modifications": [
        {
            "amino_acid": "C",
            "position": "anywhere",
            "is_static": true,
            "delta": 57.021464
        },
        ...
    ],
    "limit": 10,
    "offset": 10,
    "taxonomy_id": 7955,
    "proteome_id": "UP000000437",
    "is_reviewed": true
}

output (application/json)

{
    "peptides": [
        {
            "mass": 950.537157588,
            "sequence": "VRAMAIYK",
            "length": 8,
            "number_of_missed_cleavages": 1,
            "metadata": {
                "is_swiss_prot": true,
                "is_trembl": true,
                "taxonomy_ids": [34862, ...],
                "unique_taxonomy_ids": [34862, ...],
                "proteome_ids": ["UP000326062", ...]
            }
        },
        ...
    ],
    "count": 19
}

output (application/octet-stream)

Bytestream which contains one peptide in JSON-format per line.

{"mass":859.494958413,"sequence":"RAMELLK","is_swiss_prot":true,"is_trembl":true,"taxonomy_ids":[8032,30455,...],"unique_taxonomy_ids":[30455,194338,...],"proteome_ids":["UP000261480","UP000001038",...]}
....

output (text/plain))

Text stream in fasta format.

>macpepdb|859494958413_RAMELLK
RAMELLK
...

output (text/csv)

"mass","sequence","in_swiss_prot","in_trembl","taxonomy_ids","unique_for_taxonomy_ids","proteome_ids"
859.491587572,"AAFPQKKA","false","true","61819,8014","8014","None,UP000261340"
...

Calculate theoretical mass

http://localhost/api/peptides/mass/<SEQUENCE>

additional headers

Content-Type: application/json

example

http://localhost/api/peptides/mass/VQDDTK

output

{
    "mass": 704.334083868
}

Digest peptide

url

http://localhost/api/peptides/digest

method

POST

additional headers

Content-Type: application/json

body (JSON)

keys:

sequence: string
maximum_number_of_missed_cleavages: unsigned int
minimum_peptide_length: unsigned int
maximum_peptide_length: unsigned int
do_database_search: bool, if true the resulting peptides will be matched against the database

ouput

{
    "database": [
        {
            "mass": 588.286739698,
            "sequence": "DAQAGK",
            "length": 6,
            "number_of_missed_cleavages": 0,
            "metadata": null
        },
        ...
    "digestion": [
        ...
    ],
    "
Body
Cookies
Headers
(6)
Test Results
Status:
": 101
}

Taxonomies

Search

url

http://localhost/api/taxonomies/search

method

POST

additional headers

Content-Type: application/json

body (JSON)

keys:

query: int|string (If this is an integer, the API searches for an exact ID. If this is a string, the API search for a scientific name. You can use '*' as wildcard.)

example:

{
    "query": 71399
}

{
    "query": "*laviciniaceae"
}

output

Both examples will lead to

[
    {
        "id": 71399,
        "name": "Pallaviciniaceae"
    }
]

note

If the given ID was merged with another one, only the new ID will reported. For example a search for ID 56884 would result in the same output, because it was merged with 71399.

Lookup by ID

url

http://localhost/api/taxonomies/<ID>

example

http://localhost/api/taxonomies/56884

output

{
    "id": 71399,
    "name": "Pallaviciniaceae",
    "parent": 186795,
    "rank": 4
}

note

If the given ID was merged with another one, the resulting ID will differ. The ID 56884 from the example was merged with 71399. So 71399 is reported.

Lookup sub species of taxonomy

url

http://localhost/api/taxonomies/<ID>/sub-species

example

http://localhost/api/taxonomies/71399/sub-species

output

{
    "sub_species": [
        {
            "id": 53033,
            "name": "Symphyogyna brongniartii",
            "parent": 37401,
            "rank": 23
        },
        ...
    ]
}

API

Proteins

Lookup by accession

url

ouput

Get peptides of protein

url

additional headers

output (application/json)

output (text/csv)

Digest protein

url

method

additional headers

body (JSON)

ouput

Get amino acids

url

ouput

Peptides

Lookup by sequence

url

Query parameter

ouput

Get proteins of peptide

url

ouput

Check multiple sequences for existence

url

method

body (JSON)

ouput (text/plain)

Search by mass

url

method

additional headers

body (JSON)

body (Form)

output format

output (application/json)

output (application/octet-stream)

output (text/plain))

output (text/csv)

Calculate theoretical mass

additional headers

example

output

Digest peptide

url

method

additional headers

body (JSON)

ouput

Taxonomies

Search

url

method

additional headers

body (JSON)

output

note

Lookup by ID

url

example

output

note

Lookup sub species of taxonomy

url

example

output