DATA AND SOFTWARE AVAILABILITY

The mass spectrometry data is deposited in GNPS-MassIVE at http://gnps.ucsd.edu under accession number MSV000079652 and the molecular networks were also created within this infrastructure (Wang et al 2016). The molecular network and parameters for the patient data are available at: http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=63e8945df5e94828a25e8c71e26a1f6chttp://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=07d7ee88c5f240c296468813929e2c8a

The molecular network and parameters for the patient data and data acquired on cultured microbial isolates are available at: http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=62239894791e45258ad23e6d82db9d8bhttp://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=7f6ce726d8df4ad6975bcb0c24a76e1d

The molecular network and parameters for comparison between the patient data, and public data acquired on sputum, gut and skin under the relevant mass spectrometry conditions are available at http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=f0488dde74204aac826a305a339c6513

The annotations made using the dereplication workflow are available at http://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=071cb47acc8c4a9a89003fca749f5dcf&view=view_all_annotations_DB

Sequencing data: EBI accession number is ERP051557 and it is study 11335 in Qiita