addknownsites.qmd

---
title: "Add known sites"
author: "Cox Lab"
format: 
  html:
    toc: true
    toc-depth: 4
    toc-expand: false
    number-sections: true
    number-depth: 4
editor: source
date: today
bibliography: references.bib
---

# General

-   **Type:** - Matrix Processing
-   **Heading:** - Modifications
-   **Source code:** [AddKnownSites.cs](https://github.com/JurgenCox/perseus-plugins/blob/master/PerseusPluginLib/Mods/AddKnownSites.cs)

# Brief description

Sites that are known in PhosphoSitePlus are indicated.

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===== Detailed description =====
===== Parameters =====
===== Theoretical background =====
===== Examples =====
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# Parameters

## Modification

Selected modification for which the known sites should be added (default: Phosphorylation). The modification can be selected from a predefined list:

-   Acetylation
-   Methylation
-   O-GlcNAc
-   Phosphorylation
-   Sumoyalation
-   Ubiquitination

## Uniprot column

Selected text column that contains the Uniprot identifiers (default: first text column in the matrix).

## Sequence column

Selected text column that contains the sequence windows around the sites (default: first text column in the matrix).

# Parameter window

![](images/modifications-add_known_sites-edited.png)