Welcome to ADAP-KDB Spectral Knowledgebase!
The number of metabolomics studies in public data repositories such as the NIH’s Metabolomics Data Repository (a.k.a. Metabolomics Workbench) and MetaboLights acquiring untargeted data from the liquid chromatography (LC-) and gas chromatography coupled to mass spectrometry (GC-MS) analytical platforms has been steadily growing. Accompanying this growth is the enormous number of known and unknown compounds contained in that data, providing an invaluable opportunity to harness the power of big data and allow for cross-species, cross-diseases, and cross-sample source analysis.
Toward this end, we have developed ADAP-KDB, a mass spectral knowledgebase that contains consensus GC-MS and LC-MS/MS spectra constructed from untargeted, publicly available metabolomics data. At this point, all the consensus spectra are constructed from data in the Metabolomics Workbench and spectra constructed similarly from other publicly available data repositories will be gradually added.
ADAP-KDB enables efficient sharing and aggregation of information about both known and unknown compounds across studies and laboratories and makes those compounds easily findable.
Explore NMDR studies
- Browse all consensus spectra by clicking Libraries, and then View All Consensus Spectra;
- Filter the consensus spectra by clicking Filter, entering "glucose" to the Name Search box, and clicking Filter again;
- Sort the consensus spectra clicking Average P-value column header;
- ST000419 (“Impact Of High Sugar Diet On L-Arginine Metabolism In The Lung”),
- ST000390 (“Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma”),
- ST000402 (“Impact of glucose on the central metabolome of C. minutissima”),
- and others
Search against ADAP-KDB Library
- Click Upload to upload MSP files with spectra, CSV files with feature information, mzML or mzXML files with raw MS/MS spectra, or use direct links from the Metabolomics Workbench to upload raw MS/MS data. In addition, you can combine information from MSP and CSV files.
- Click Search dropdown menu and select one of the
following options:
- Search for similar spectra for matching against library spectra based on the spectral similarity;
- Search for similar studies for matching the uploaded spectra directly against the Metabolomics Workbench studies (Experimental).
- Click Filter button to select the libraries used for the matching, and select specific species, sample source, or disease.
- Click Export button to export the library matching results.
Use one of these sample files to try the library searching: MSP file with GC-MS spectra, MSP file with LC-MS/MS spectra, or CSV file with m/z-retention time features.
Download a file, then click Upload Files, select "GC", "LC MS/MS +", or "Mass" respectively in the Chromatography type dropdown list, select the downloaded file, and click Upload. When uploading the sample CSV file, you need to specify where to find the neutral mass information by clicking Edit Metadata Fields on the upload page and putting "neutral_mass" for the Neutral Mass Field in the CSV column.
Search against In-House library
- Create an account on ADAP-KDB by clicking Log In / Sign Up.
- Upload MSP and CSV files with the library spectra/features.
- Save them as private in-house library spectra. Private means that they will not be accessible to other users, in-house means that the corresponding matches will have a higher confidence level when searched with the ontology levels, and library means that the spectra will be used for searching against.
- Search experimental spectra against the saved library.
ADAP Spectral Knowledgebase is currently being actively developed by the Du-Lab team ( https://www.du-lab.org/).
If you encounter any issues or would like to provide a feedback on your experience using ADAP Spectral Knowledgebase click here, or please contact us through the email dulab.binf@gmail.com.