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.

MzQCFile.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