Export files for GNPS
With pyOpenMS you can automatically generate all files needed for GNPS Feature-Based Molecular Networking (FBMN) and Ion Identity Molecular Networking (IIMN).
Pre-requisites are your input mzML files and a
ConsensusMap, generated by an untargeted metabolomics pre-processing workflow. Ensure that MS2 data has been mapped to the
FeatureMap objects with
IDMapper. For IIMN adduct detection must have been performed on the
FeatureMap objects during pre-processing with
First, download two example
mzML files that have been map aligned based on a feature map alignment.
from urllib.request import urlretrieve gh = "https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master" urlretrieve (gh + "/src/data/Metabolomics_1_aligned.mzML", "Metabolomics_1_aligned.mzML") urlretrieve (gh + "/src/data/Metabolomics_2_aligned.mzML", "Metabolomics_2_aligned.mzML") urlretrieve (gh + "/src/data/UntargetedMetabolomics.consensusXML", "UntargetedMetabolomics.consensusXML")
from pyopenms import * mzML_files = ["Metabolomics_1_aligned.mzML", "Metabolomics_2_aligned.mzML"] consensusXML_file = "UntargetedMetabolomics.consensusXML"
Since GNPS only works with features that contain MS2 fragmentation spectra, the first step is to filter out features from your
ConsensusMap that have no MS2 spectra annotated.
consensus_map = ConsensusMap() ConsensusXMLFile().load(consensusXML_file, consensus_map) filtered_map = ConsensusMap(consensus_map) filtered_map.clear(False) for feature in consensus_map: if feature.getPeptideIdentifications(): filtered_map.push_back(feature) consensusXML_file = "filtered.consensusXML" ConsensusXMLFile().store(consensusXML_file, filtered_map)
Now you can export your all files for FBMN and IIMN.
# for FFBM GNPSMGFFile().store(String(consensusXML_file), [file.encode() for file in mzML_files], String("MS2data.mgf")) GNPSQuantificationFile().store(consensus_map, "FeatureQuantificationTable.txt") GNPSMetaValueFile().store(consensus_map, "MetaValueTable.tsv") # for IIMN IonIdentityMolecularNetworking().annotateConsensusMap(consensus_map) IonIdentityMolecularNetworking().writeSupplementaryPairTable(consensus_map, "SupplementaryPairTable.csv")