GC-MS Assay File Default Structure v1.0¶
Download file template as zip file or txt file
| Header | Column Structure | Constraints | Description |
Examples |
|---|---|---|---|---|
| Sample Name | single column | Required MinLength: 1 Controls |
A unique identifier from a particular source (a batch of samples can have a unique Sample name as identified in the Sample table). It’s usually associated with an output spectral data filename. | ADG10003u_007 Example_1 Sample1 |
| Protocol REF | single column | Required Default: Extraction |
This is the column marking the start of data pertaining to Extraction protocol. The 'Extraction' term MUST be present in all rows of this column. | Extraction |
| Parameter Value[Post Extraction] | single column | This how the sample was extracted into a solvent prior to being injected into the analytical instrument of choice. | 2 ml ethyl acetate | |
| Parameter Value[Derivatization] | single column | Controls | If the sample has been subjected to chemical modification prior to injection. | sylilation |
| Extract Name | single column | This can be, but doesn’t have to be, the same as the ‘Sample Name’. | Example_1 | |
| Protocol REF | single column | Required Default: Chromatography |
This is the column marking the start of data pertaining to Chromatography protocol. The 'Chromatography' term MUST be present in all rows of this column. | Chromatography |
| Parameter Value[Chromatography Instrument] | ontology column | Required MinLength: 5 |
Add the full name of the instrument you used for the Chromatographic part of this assay, including the manufacturer and model number as reported in manufacturer’s brochures, user manuals, or on their website. | Shimadzu GCMS-QP2010 Ultra |
| Parameter Value[Autosampler model] | single column | Add the full name of the autosampler used for the Chromatographic part of this assay, including the manufacturer and model number as reported in manufacturer’s brochures, user manuals or website. | ||
| Parameter Value[Column model] | single column | Required MinLength: 5 |
Manufacturer, model number and dimensions of the column model. | Zebron ZB-AAA GC(10 m x 0.25 mm; Phenomenex) |
| Parameter Value[Column type] | single column | Required MinLength: 5 |
Polarity of column used. This information can be found on the manufacturer’s website. | low polarity medium polarity high polarity |
| Parameter Value[Guard column] | single column | Manufacturer, model number and dimensions in the format shown in the examples. | Z-Guard (0.25 mm x 10 m; Zebron) | |
| Labeled Extract Name | single column | Leave blank if you don’t have one. | ||
| Label | ontology column | If you used a chemical or biochemical marker in the sample such as a radioactive isotope of fluorescent dye which is bound to a material in order to make it detectable in an analytical instrument then enter it here. | ||
| Protocol REF | single column | Required Default: Mass spectrometry |
This is the column marking the start of data pertaining to Mass spectrometry protocol. The 'Mass spectrometry' term MUST be present in all rows of this column. | Mass spectrometry |
| Parameter Value[Scan polarity] | single column | Required MinLength: 1 Controls |
Values should identical within each assay. If you have ‘positive’ or ‘negative’ values in the same assay then split them into separate ‘positive’ and ‘negative’ assays. | positive negative |
| Parameter Value[Scan m/z range] | single column | Required MinLength: 1 |
The range used in the assay. | 50-400 |
| Parameter Value[Instrument] | ontology column | Required MinLength: 1 |
Add the full name of the mass spectrometer/detector you used for this LC/MS assay, including the instrument manufacturer and model number as reported in manufacturer’s brochures, user manuals, or on their website. | Thermo Electron Trace DSQ |
| Parameter Value[Ion source] | ontology column | Where applicable to the instrument. | electron ionization | |
| Parameter Value[Mass analyzer] | ontology column | Controls | The analyser/detector of the mass fragments generated during the assay. | quadrupole |
| MS Assay Name | single column | Controls | This can be, but doesn’t have to be, the same as the ‘Sample Name’ | Assay_1 Run_1 Sample1 |
| Raw Spectral Data File | single column | This is where you should enter the Raw (unprocessed) MS data files. Please add full path of the file in the cell. | FILES/myfilename1.raw FILES/RAW_FILES/myfilename1.raw |
|
| Protocol REF | single column | Default: Data transformation | This is the column marking the start of data pertaining to Data transformation protocol. The 'Data transformation' term MUST be present in all rows of this column. | Data transformation |
| Normalization Name | single column | These should contain the normalization data files preferably as an Excel spreadsheet file. If you don’t have these then leave the cells/column blank. | normalized-data.xlsx | |
| Derived Spectral Data File | single column | If your data has been transformed into one of the open-source raw data formats e.g. mzML , CDF, or any other converted file, then add them here. Please add full path of the file in the cell. | FILES/myfilename1.mzML FILES/DERIVED_FILES/myfilename1.mzML |
|
| Protocol REF | single column | Required Default: Metabolite identification |
This is the column marking the start of data pertaining to Metabolite identification protocol. The 'Metabolite identification' term MUST be present in all rows of this column. | Metabolite identification |
| Data Transformation Name | single column | These should contain the data transformation files. | ||
| Metabolite Assignment File | single column | Required MinLength: 1 |
A TSV file containing information about the metabolites investigated in the study. Information regarding database accession IDs , where in the spectra the metabolite is found and data pertaining to its abundance within the study samples should be in this file. | m_MTBLS1_GC-MS_positive__metabolite_profiling_v2_maf.tsv |