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.

from pyopenms import *

from urllib.request import urlretrieve

gh = "https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master"

# minimal required informations are input_file, output_file and a MSExperiment
input_file = "QCCalculator_input.mzML"
output_file = "result.mzQC"

# load mzML file in MSExperiment
urlretrieve(gh + "/src/data/QCCalculator_input.mzML", "input.mzML")
exp = MSExperiment()
MzMLFile().load("input.mzML", exp)

# prepare metadata for the mzQC file (optional but recommended)
contact_name = "name of the person creating the mzQC file"
contact_address = "contact address (mail/e-mail or phone) of the person creating the mzQC file"
description = "description and comments about the mzQC file contents"
label = "unique and informative label for the run"

feature_map = FeatureMap()
# OPTIONAL: load featureXML file in FeatureMap()
urlretrieve(
    gh + "/src/data/FeatureFinderMetaboIdent_1_output.featureXML",
    "features.featureXML",
)
FeatureXMLFile().load("features.featureXML", feature_map)

prot_ids = []  # list of ProteinIdentification()
pep_ids = []  # list of PeptideIdentification()
# OPTIONAL: get protein and peptide identifications from idXML file
urlretrieve(gh + "/src/data/OpenPepXL_output.idXML", "ids.idXML")
IdXMLFile().load("ids.idXML", prot_ids, pep_ids)

# create MzQCFile object and use store() to calculate and write the mzQC file
mzqc = MzQCFile()
mzqc.store(
    input_file,
    output_file,
    exp,  # minimal required information
    contact_name,
    contact_address,
    description,
    label,  # optional, but recommended, can be empty
    feature_map,
    prot_ids,
    pep_ids,
)  # optional, can be empty