# DDA quantification - peptidoform level (QExactive)

This module compares the sensitivity and quantification accuracy for data acquired with data-dependent acquisition (DDA) on a Q Exactive HF-X Orbitrap (Thermo Fisher).
It is based on the DDA quantification module "ion-level" described [here](#2-quant-lfq-ion-dda). Data and metrics are the same, the difference is that in this module we focus on peptidoform quantities summarised from the precursor ion quantities. 

## How to use

Click [here](https://proteobench.cubimed.rub.de/Quant_LFQ_DDA_peptidoform) if you want to submit your results or when you want to explore the module.

## Important Tool-specific settings

Table 2 provides an overview of the required input files for public submission.

**Table 2. Overview of input files required for metric calculation and public submission**

| Tool | Input file | Parameter File |
|---|---|---|
| Custom | custom_input.tsv |  |
| PEAKS | lfq.features.csv | *.txt |
| WOMBAT | *.csv | config.yaml |

**We are working on the documentation: more information comming soon.**