To represent quantification and extract meaningful insight there are two file formats that we define:
- Minimal Feature Input Format (MFIF) - This describes feature quantification
- Annotation Format - This describes the experimental design and conditions to meaningfully compare
These two files are used for creating a reanalysis for MassIVE.quant as well as enabling you to compute statistics with the MSstats workflow.
## MFIF Documentation
This describes the quantification format that will be required. The format must be tab separated.
| Header | Description | Required |
|---|---|---|
| Protein | Name of the protein | Proteomics |
| Unmodified Peptide | Sequence of peptide without modifications | Proteomics |
| Modified Peptide | Sequence of peptide including modifications | Proteomics |
| Compound | Name of the compound | Metabolomics |
| Feature ID | Feature ID | Metabolomics |
| m/z | Mass to charge ratio | All |
| Charge | Precursor charge | All |
| Run | Sample/Run Name | All |
| Intensity | Intensity for the feature | All |
Annotation Format
| Header | Description | Required |
|---|---|---|
| Run | File name for sample | Yes |
| Subject | An individual from whom multiple samples maybe aquired for the purpose of the study. | No |
| Cohort | A set of subjects aggregated for the purpose of the study | Yes* |
| Condition | Original dataset study variable | Yes* |
| TimePoint | Different time points within the same experiment | Yes* |
| BioReplicate | Biological replicate | Yes |
| Experiment | Technical replicate | Yes |
| Fraction | Fraction number | No |
| Disease | Disease name | Yes* |
| Tissue | Tissue name | Yes* |
| Species | Species name | Yes* |
| Enzyme | Enzyme name | No |
| Notes | Other notes | No |
| Dataset | MassIVE Dataset Accession | No (Only for Reanalysis Attachement) |
*One of the following must be in the file.