MsLookup Webservice

The MSLoopkup web service is a Restful API that provides a programatic interface to access to peptide evidences previously identified in mass spectrometry experiments.

Note

The API is published in the following URL: https://www.ebi.ac.uk/pride/multiomics/ws

Mass spectrum JSON structure

The MSLookup service provides mass spectrometry evidences for peptides, with special focus on modified peptides (PTMs - posttranslational modifications) and single aminoacid variants. The structure of the spectra provided on each endpoint is the following:

{
  "id": "NIST:cptac2_human_hcd_itraq_selected_part1_2015.msp:index:80003",
  "usi": "NIST:cptac2_human_hcd_itraq_selected_part1_2015.msp:index:80003",
  "pepSequence": "AQLGVQAFADALLIIPK",
  "proteinAccessions": [ "P40227-2", "ENSP00000275603.4"],
  "geneAccessions": [CCT6A","ENSG00000146731.11","ENST00000335503.3"],
  "precursorMz": 514.8157,
  "precursorCharge": 4,
  "projectAssays": null,
  "pxProjects": null,
  "species": [],
  "modifications": [
      {
        "neutralLoss": null,
        "positionMap": [
           {
             "key": 0,
             "value": []
           },
           {
             "key": 16,
             "value": []
           }
         ],
        "modification": {
           "cvLabel": "UNIMOD",
           "accession": "UNIMOD:214",
           "name": "iTRAQ4plex",
           "value": "144.102063"
        },
       "attributes": null
      }
  ],
  "masses": [145.1084,199.1806,458.2939],
  "intensities": [5123.7,6716.8,2049.7],
  "retentionTime": null,
  "properties": null,
  "missedCleavages": 0,
  "annotations": null,
  "qualityEstimationMethods": [],
  "text": null
}

Main spectra attributes

The mass spectrum attributes can be divided in three main groups:

• biology properties:

  • Protein accessions in ENSEMBL and UNIPROT that contains the corresponding peptides; gene accessions which represent a list of gene names, gene and transcript accessions from ENSEMBL that contains the corresponding peptides.
  • Post-translational modifications: a list of post-translational modifications identified by mass spectrometry including position, monoisotopic mass, and UNIMOD accession if available.
  • Additional metadata: species, sample conditions, tissue, cell-line, proteomeXchange project accessions.

• mass spectrometry properties: Spectrum information including (precursor mz, charge and peak list), additional information such as retention time and missed-cleavages.
• statistical assessment: additional quality and statistical assessment scores such as search engine scores, p-values, q-values.

If the information is not available empty lists or null values are provided.