Understanding Proteomics Output Files

Published

Jun 2026

This chapter explains the key result files used in downstream proteomics interpretation.

Protein Abundance Table

The abundance table contains quantified protein-level values across samples.

Differential Result Table

The differential result table summarizes changes between conditions.

Common columns include:

protein_id
gene_symbol
protein_name
log2FC
pvalue
padj
comparison

Key Interpretation Columns

log2FC: direction and magnitude of change
pvalue: statistical evidence before multiple testing correction
padj: adjusted p-value or false discovery rate
protein_id: protein identifier
gene_symbol: mapped gene symbol

# Understanding Proteomics Output Files

This chapter explains the key result files used in downstream proteomics interpretation.

## Protein Abundance Table

The abundance table contains quantified protein-level values across samples.

## Differential Result Table

The differential result table summarizes changes between conditions.

Common columns include:

```text
protein_id
gene_symbol
protein_name
log2FC
pvalue
padj
comparison
```

## Key Interpretation Columns

- `log2FC`: direction and magnitude of change
- `pvalue`: statistical evidence before multiple testing correction
- `padj`: adjusted p-value or false discovery rate
- `protein_id`: protein identifier
- `gene_symbol`: mapped gene symbol