To represent quantification and extract meaningful insight there are two file formats that we define:

  1. Minimal Feature Input Format (MFIF) - This describes feature quantification
  2. 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.

Example File

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

Example File

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.