File format:
Each technical replicate for each biological sample will have a separate file. The metadata will be specified at the time of uploading the file through the front end. The file should be tab-delimited and should have the following format:
Column Heading | What to store in each column | Requirement (Required or Optional) |
---|---|---|
Name | metabolite name | Required |
Ret_Time | Retention Time | Required |
Peak_Ion | Peak ion | Required |
Value | Intensity or normalized intensity of the metabolite | Required |
Software::Annotation | The metabolite annotation from the software | Optional |
Software::Library | The library matched for the software | Optional |
Software::Field_name | The field name for a specific software. There can be one or more field names from each software. | Optional |
Where
- Name --- is the metabolite name.
If it is an unknown metabolite, then please use the following naming convention: “JS-G1-P1-0009570-0130000”
- JS --- John Smith. Initials of the project PI;
- G1 --- protocol used. Here ‘G’ corresponds to GC/MS and ‘1’ corresponds to the first protocol used for GC/MS. If you have data for more than one protocols for GC/MS then it will be like G1, G2 and so on. Similarly for LC/MS it will be like L1, L2 and so on.
- P1 --- extraction protocol. ‘P’ corresponds to polar and ‘1’ corresponds to first extraction protocol. For lipid (non-polar) extractions for GC/MS, it will be like L1, L2 and so on.
- Number1 --- the retention time for the metabolite. The format is ####.###. e.g. retention time 9.57 will be 0009570.
- Number2 --- major peak ion for the metabolite. The format is also ####.###. e.g. Peak_ion 130 will be 0130000.
- Ret_Time: retention time for the metabolite.
- Peak_Ion: major peak ion for the metabolite.
- Value: intensity value for the metabolite. It could be normalized or not.
- Software::Library: the metabolite name is matched against certain library using the software.
- Software::Annotation: The annotation for the metabolite using the software.
- Software::Field_name: The value of a field name measured or matched by using the software.
The file can contain more than one software. For each software it can have only one annotation and/or one library. But it can have many qualifiers.
File names:
Please name your files using only the following characters “a–z”, “A–Z”, “0–9” and “_”. Connect parts of the name with underscores. Please have the same name for “.cdf” and “.txt” files for the same sample. For example, xxx_yy_zzz.txt and xxx_yy_zzz.cdf correspond to one sample for which xxx_yy_zzz.cdf is the raw data file and xxx_yy_zzz.txt is the processed data file.
Here is an example of the format for processed data file:Name | Ret_Time | Peak_Ion | Value |
---|---|---|---|
JS-G1-L1-0015796-0228000 | 15.796 | 228 | 8723 |
JS-G1-L1-0016420-0160000 | 16.42 | 160 | 13184 |
Ethanolamine-N,N,O-TMS | 16.545 | 174 | 1457471 |
Phosphoric acid TMS | 16.598 | 299 | 71719 |
Glycerol TMS | 16.622 | 205 | 1286866 |
Malate | 21.5 | 423 | 175 |
Another example:
Name | Ret_Time | Peak_Ion | Value | Xcalibur::library | Xcalibur::RSI_score | Xcalibur::probability_score | AMDIS::purity_percent | Amdis::Annotation | Xcalibur::Annotation |
---|---|---|---|---|---|---|---|---|---|
L-Aspartic Acid | 22.1 | 350 | 0.116008 | Golm | 907 | 20.2 | 80 | EIQTMS_N12C_SD1_1525.1_1267BK12_L-Aspartic acid (3TMS) | L-aspartic acid |
Leucine | 15.75 | 158 | 0.007251 | UNR |   |   |   |   | Leucine |
L-Glutamine | 27.89 | 156 | 0.57555 | UNR | 925 | 75.02 | 92 | EIQTMS_N12C_ATHL_1784.8_3038BN18_L-Glutamine (3TMS) | L-Glutamine |
Tyrosine | 31.09 | 218 | 0.015173 | UNR |   |   | 21 | L-Tyrosine, N,O-bis(trimethylsilyl)-, trimethylsilyl ester | Tyrosine |