Quality Control

With MzQCFile pyOpenMS provides a tool to export quality control data from an experiment to a mzQC file following the HUPO-PSI specifications. MzQC is a reporting and exchange format for mass spectrometry quality control data in JSON format.

store() requires, besides the input_file and output_file path, at least a MSExperiment. Optionally, a FeatureMap and/or lists of ProteinIdentification and PeptideIdentification can be provided to calculate additional proteomics and metabolomics quality metrics.

 1from pyopenms import *
 3from urllib.request import urlretrieve
 5gh = "https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master"
 7# minimal required informations are input_file, output_file and a MSExperiment
 8input_file = "QCCalculator_input.mzML"
 9output_file = "result.mzQC"
11# load mzML file in MSExperiment
12urlretrieve(gh + "/src/data/QCCalculator_input.mzML", "input.mzML")
13exp = MSExperiment()
14MzMLFile().load("input.mzML", exp)
16# prepare metadata for the mzQC file (optional but recommended)
17contact_name = "name of the person creating the mzQC file"
18contact_address = "contact address (mail/e-mail or phone) of the person creating the mzQC file"
19description = "description and comments about the mzQC file contents"
20label = "unique and informative label for the run"
22feature_map = FeatureMap()
23# OPTIONAL: load featureXML file in FeatureMap()
25    gh + "/src/data/FeatureFinderMetaboIdent_1_output.featureXML",
26    "features.featureXML",
28FeatureXMLFile().load("features.featureXML", feature_map)
30prot_ids = []  # list of ProteinIdentification()
31pep_ids = []  # list of PeptideIdentification()
32# OPTIONAL: get protein and peptide identifications from idXML file
33urlretrieve(gh + "/src/data/OpenPepXL_output.idXML", "ids.idXML")
34IdXMLFile().load("ids.idXML", prot_ids, pep_ids)
36# create MzQCFile object and use store() to calculate and write the mzQC file
37mzqc = MzQCFile()
39    input_file,
40    output_file,
41    exp,  # minimal required information
42    contact_name,
43    contact_address,
44    description,
45    label,  # optional, but recommended, can be empty
46    feature_map,
47    prot_ids,
48    pep_ids,
49)  # optional, can be empty