MetaboBank
Data files
- Make sure the file names are constructed only from alphanumerals [A-Z,a-z,0-9], underscores [_], hyphens [-] and dots [.], with no whitespaces, brackets, other punctuations or symbols.
- Filename should be unique in a study.
- Files archived by tar or zip per study or sample, are accepted.
- Subdirectories can be included.
- User’s local filepaths may be recorded in vendor raw data files. Please do NOT include personal information in vendor raw files.
Mass spectrometry (MS)
Raw data file
Raw data files generated by measurement platforms (vendor raw).
MetaboBank accepts open standard files such as mzML as raw data files.
Enter raw data filenames in “Raw Data File” column of SDRF.
If there are more than one file for a sample (SDRF one row), group them by tar or zip per sample.
User’s local filepaths may be recorded in vendor raw data files. Please do NOT include personal information in vendor raw files.
Processed data file
Analyzed data or summary on which conclusion of associated paper is based.
Enter processed data filenames in “Processed Data File” column of SDRF.
If there are more than one file for a sample (SDRF one row), group them by tar or zip per sample.
Metabolite assignment file
Submit information of identified metabolites in Metabolite assignment file (MAF). Please see Metabolite assignment file for details.
MS MAF excel (download)
Image file
For the MS imaging experiments, submit image files. Enter image data filenames in “Image Data File” column of SDRF. If there are more than one file for a sample (SDRF one row), group them by tar or zip per sample. Include configuration files for imaging experiments as much as possible.
NMR
Raw data file
Raw data files generated by measurement platforms.
MetaboBank accepts open standard files such as nmrML as raw data files.
Enter raw data filenames in “Raw Data File” column of SDRF.
If there are more than one file for a sample (SDRF one row), group them by tar or zip per sample.
Include configuration files for NNR experiments as much as possible.
Processed data file
Analyzed data or summary on which conclusion of associated paper is based.
Enter processed data filenames in “Processed Data File” column of SDRF.
If there are more than one file for a sample (SDRF one row), group them by tar or zip per sample.
Metabolite assignment file
Submit information of identified metabolites in Metabolite assignment file (MAF). Please see Metabolite assignment file for details.
NMR MAF excel (download)
Metabolite assignment file
The metabolite assignment file (MAF) is recommended to include all metabolites/unknowns/features identified or annotated within the study. Please complete the table with as much information as possible. Sample names need to be added in the columns to the right of the table, in each column sample values per metabolite should be included.
The fixed MAF columns are as follows.
| Column | Description | Example | Technology type |
|---|---|---|---|
| database_identifier | Database identifier for metabolite. ChEBI ID is recommended. This is optional field. | CHEBI:16919 | MS and NMR |
| chemical_formula | Chemical formula of metabolite. This is optional field. | C4H9N3O2 | MS and NMR |
| smiles | SMILES of metabolite. This is optional field. | CN(CC(O)=O)C(N)=N | MS and NMR |
| inchi | INCHI key of metabolite. This is optional field. | InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) | MS and NMR |
| metabolite_identification | Identified metabolite name. | creatine | MS and NMR |
| metabolite_class | Class of metabolite | flavonoids | MS and NMR |
| mass_to_charge | The mass to charge (m/z) ratio. | 132.0765 | MS and NMR |
| fragmentation | Fragmentation | 132,0870 l 90,0617 l 87,0618 | MS |
| modifications | Chemical modifications. | [M+H]+ | MS |
| charge | Charge | 1 | MS |
| retention_time | Retention time | 0.85 | MS |
| chemical_shift | Chemical shift of peak. | NMR | |
| multiplicity | Multiplicity of peak | NMR | |
| taxid | The NCBI taxonomy id for the organism from which the metabolite was obtained. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi | 9606 | MS and NMR |
| species | Species name of the NCBI taxonomy. | Homo sapiens | MS and NMR |
| database | The database name used for metabolite identification. | CHEBI | MS and NMR |
| database_version | The database version used for metabolite identification. | MS and NMR | |
| reliability | Reliability. Identification confidence of the metabolite. See https://github.com/MSI-Metabolomics-Standards-Initiative/CIMR | MSI:1 | MS and NMR |
| search_engine | Search engine | MS and NMR | |
| search_engine_score | Search engine score | MS and NMR | |
| peak_identifier | MS and NMR |