DMA Data and Results

dmadb.bham.ac.uk/data_and_results_summary/

Compound annotations

All compound annotations derived from the DMA are summarised at dmadb.bham.ac.uk/compounds/.

The annotations have been summarised across all of the DMA assays that have been analysed with Galaxy DMA workflow but also merged with some external annotation sources including annotation via GNPS, mzCloud and annotations from NMR and GC-MS.

As the Deep Metabolome Annotation has only been done on one organism (Daphnia magna) - this section is currently only summarising the annotation for D. magna.

The compounds are distinguished by a unique InChiKey and can filtered and searched by the following columns

Column name	Description
Monoisotopic exact mass	The monoisotopic exact mass of the annotation (derived from PubChem)
Inchikey	InChIKey - International Chemical Identifier Key
Inchi	InChi - International Chemical Identifier
Smiles	SMILES - Simplified molecular-input line-entry system
Compound name	Compound name of annotation
Natural product inchikey1	Check if the first component of the InChIKey of the metabolite annotation matches that of the Natural products listed from the “COCONUT - the COlleCtion of Open Natural ProdUcT”
Pubchem cids	List of all PubChem CIDs found for this InChiKey
Hmdb ids	List of all HMDB IDs found for this InChiKey
Kegg ids	List of all KEGG IDs found for this InChiKey
Chebi ids	List of all ChEBI IDs found for this InChiKey
Kingdom	Kingdom compound classification from ClassyFire
Superclass	Superclass compound classification from ClassyFire
Subclass	Subclass compound classification from ClassyFire
Direct parent	Direct parent compound classification from ClassyFire
Molecular framework	Molecular framework of compound from ClassyFire
Predicted lipidmaps terms	Predicted lipidmaps terms of compound from ClassyFire
Extraction	DMA liquid phase extraction protocol(s) the annotation observed in
Spe	DMA Solid Phase Extraction (SPE) protocol(s) the annotation observed in
Spe frac	DMA SPE fraction the annotation observed in
Chromatography	DMA chromatography protocol(s) the annotation observed in
Measurement	DMA measurement (LCMSMS, DIMSn, GCMS, NMR) protocol(s) the annotation observed in
Polarity	The mass spectrometry ionisation polarity the annotation observed in
Nmrbool	Boolean - true if annotation observed using NMR measurement
Gcmsbool	Boolean - true if annotation observed using GC-MS measurement
Smbool	Boolean - true if annotation observed using LC-MS/MS or DIMSn spectral matching to library spectra
Metfragbool	Boolean - true if annotation observed using MetFrag annotation software for LC-MS/MS or DIMSn data
Siriusbool	Boolean - true if annotation observed using SIRIUS CSI:FingerID annotation software for LC-MS/MS or DIMSn data
Siriusbool	Boolean - true if annotation observed using SIRIUS CSI:FingerID annotation software for LC-MS/MS or DIMSn data
Mzcloudsmbool	Boolean - true if annotation observed using mzCloud database for LC-MS/MS or DIMSn spectral matching annotation
Galaxysmbool	Boolean - true if annotation observed using Galaxy workflow for LC-MS/MS or DIMSn spectral matching annotation
Gnpssmbool	Boolean - true if annotation observed using GNPS workflow for LC-MS/MS or DIMSn spectral matching annotation
Msi level	The Metabolomics Standards Initiative (MSI) level for the annotation

Fig 1. Browse and filter compound annotations

Individual compounds can be double clicked on to open up a page summarising where the annotations has been observed (currently only showing information related to DMA of D. magna)

Fig 2. Further details of compound annotations

Browse raw data files

The raw (and .mzML) data files can be browsed, filtered and downloaded from dmadb.bham.ac.uk/mfile_summary/.

Fig 3. Browse, filter and download raw (and .mzML) mass spectrometry data files

Browse analysis datasets

The DMA Galaxy workflow outputs as a result an SQLite file for each DMA assay that has been analysed (incorporating the annotation and peak information from LC-MS, LC-MS/MS, DIMS and DIMSn data).

Each of these SQLite data files can be individually inspected through the DMAdb interface from dmadb.bham.ac.uk/dataset_summary/.

To access this information a user needs to have an account (i.e. a guest cannot access)

First the user can select the processed data file to choose from via using the filter option and can choose from the following options:

Column name	Description
Assay name	The DMA assay from which the data was derived from
Polarity	The mass spectrometry ionisation polarity from which the data was derived from
Metabolite standard	Boolean - if true, then the data and results are for a metabolite reference standard mix (e.g. the assay was used for validation purposes rather that measuring the metabolite directly in an organism)
Fractionation	Boolean - if true, then the data and results are from the DMA fractionation assays and include information and annotations for both LC-MS, LC-MS/MS and the DIMS and DIMSn of LC fractions

Fig 4. Select an filter analysis datasets

For each dataset a annotations and peaks can then be inspected which in turn can be filtered.

Fig 4. View (an filer) annotations and peaks from a specific analysis dataset

See below for definitions of columns:

Column name	Description
Inchikey	InChIKey - International Chemical Identifier Key
Compound name	Compound name of annotation
Ms type	Mass spectrometry type (Fractionation data can either be “lcms” or “dims” if from the LC fractions)
Sid	Scan peak id (unique id for this dataset for the “dims” peak)
Grpid	Grouped peak id (unique id for this dataset for the grouped LC-MS peak)
Grp name	The name given by XCMS to the grouped LC-MS peak
Mz	m/z of the peak
Rt	Retention time of the peak
Well	If the peak from an LC fraction, the well from which the DIMS data was taken
Sm score	Spectral matching score - values between 0 to 1 (dpc)
Metfrag score	MetFrag annotation score (weighted score - see Galaxy workflow) - values between 0 to 1
Sirius score	SIRIUS CSI:FingerID score (the ranking from SIRIUS CSI:FingerID was converted to a value between 0 to 1 using a “minmax” normalisation.)
Ms1 lookup score	A binary score, where 1 signifies a match of the a calculated neutral mass to a public metabolite database and 0 signifies there was no match
Biosim max score	A tanimoto similarity analysis between the structure of the annotated compound against a preselected list of compounds known to be from “biology” from HMDB
Wscore	A weighted score between 0 to 1 of - see the DMA Galaxy workflow for details of the weighting
Rank	A rank derived from the Wscore
Adduct overall	All adducts used to calculate the annotation

The weighted scores for “Sm score”, “MetFrag score”, “Sirius score”, “Ms1 lookup score” and “Biosim max score” are all show in the table with the suffix “wscore”. See the DMA Galaxy workflow for details of the weightings used.

Views of the extracted ion chromatogram and fragmentation data can also be viewed.

The fragmentation data shown for both the individual spectra, the averaged spectra within the a file (intra) and the averaged spectra across all files (inter.)

Fig 6. view EIC and fragmentation data

The mass spectrometry fragmentation based fragmentation annotation results from DMA Galaxy workflow can also be viewed in further detail (Spectral matching, MetFrag and SIRIUS CSI:FingerID)

Fig 7. View the mass spectrometry fragmentation based fragmentation annotations derived from the DMA Galaxy workflow (Spectral matching, MetFrag and SIRIUS CSI:FingerID)

Exact mass search

A registered user can search all the annotations in batch via monoisotopic exact masses dmadb.bham.ac.uk/search_mono/.

Fig 8. Search monoisotopic exact mass of annotations

The results are stored in the Monoisotopic exact mass search results section.

Where each row corresponds to batch query and the columns provide details of the parameters used for the search

Fig 9. View all results from monoisotopic exact mass searches

The individual matches from the search can then be inspected within the match table. Where each row corresponds to a single match between a query monoisotopic mass and a monoisotopic mass within the available annotations in DMAdb.

The match table includes the relevant ppm difference of the queried mass and the mass in the library, as well as all the information regarding the compound detailed in dmadb.bham.ac.uk/compounds/

Column name	Description
Ppm tolerance	PPM tolerance used as parameter for search
User	User who performed the search
Ppmdiff	The PPM difference between the query mass and the mass in DMAdb

Fragmentation spectra search

A registered user can search query fragmentation spectra against all the fragmentation spectra within DMAdb, see dmadb.bham.ac.uk/search_frag/.

The DMAdb library spectra that can be searched consist of all the averaged spectra from the LC-MS/MS and DIMSn data.

For the LC-MS/MS fragmentation spectra this includes the averaged spectra within a file (intra) and the averaged spectra across the files (inter).

By default the datasets containing the metabolite reference standards will be avoided but they can be optionally included.

Fig 10. Search query fragmentation

Each set of search results are saved in the Fragmentation search results section.

Fig 11. View all results from fragmentation searches

The individual matches from the search can then be inspected within the match table. Where each row corresponds to a single match between the query fragmentation spectra and the fragmentation spectra within DMAdb.

See below for descriptions of the match columns

Column name	Description
Dpc	Dot product cosine match result
Q prec mz	The query precursor m/z (provided by user)
L prec mz	The library precursor m/z (from the DMAdb spectra)
Ppm diff prec	PPM difference between query and library precursor
Rt	Retention time of library spectra
Well	The well fraction of the library spectra, if library spectra from LC-MS fractionation experiment
Dataset pid	Library spectra identifier from within SQLite file for this dataset specific to the LC-MS/MS data
Dataset sid	Library spectra identifier from within SQLite file for this dataset specific to the DIMSn data
Spectrum type	Library spectra spectrum type, i.e. if the data is LC-MS/MS averaged (intra or inter) or averaged from DIMSn data
Spectrum details	Library spectra further details of the library spectra if available
Dataset	The DMAdb id of the analysis dataset which the library spectra originated from
Name	The assay name associated with this library spectra
Sqlite	The link to the SQLite analysis dataset which the library spectra originated from (note this might not be available for download depending on access issues)
Top spectral match	Top spectral match result for this library spectra
Top metfrag	Top MefFrag results for this library spectra
Top sirius csifingerid	Top SIRIUS CSI:FingerID result for this library spectra
Top combined annotation	Top combined annotation (see DMA Galaxy workflow details for combining approach) for this library spectra
Top wscore	Top weighted score (see DMA Galaxy workflow details for weighting approach) for this library spectra

Individual matches can be inspected in more detail, see below. Where the spectral match plot can be viewed between the query and the matched library spectra. Further details of the annotation results of the library spectra is provided as well.

Fig 12. Further details for spectral match

Upload (admin only)

Admin users can upload analysis datasets via the Upload analysis datasets and a summary list of compounds via the Upload compounds section.