<p>There are multiple protein isoforms that the gene <em>may</em> encode. The hyphen-number after the Uniprot ID represents the isoform —in a Uniprot you find the detail of these at the bottom.
The canonical isoform in Uniprot is the most likely one to be biologically relevant, while in NCBI and Ensembl it is the longest.
In a limited amount of case multiple isoforms are biologically relevant.
For the sake of sanity most variant annotation tools have a <code>canonical</code> argument to use the canonical.</p>

CC BY-SA 4.0
2022-12-11T17:43:46.647Z
2022-12-11T17:43:46.647Z
Matteo Ferla
<p>According to a proteomics researcher at the NIH:</p>
<ul>
<li><code>proteins</code> column contains uniprot IDs.</li>
<li><code>position within proteins</code> column are the starting position of each ID.</li>
<li><code>position</code> is the <em>leading</em> protein</li>
</ul>

CC BY-SA 4.0
2022-07-13T19:23:40.803Z
2022-07-13T19:23:40.803Z
Kermit
<p>The data below is coming from a <strong>MaxQuant</strong> post-translational protein modification (PTM) site file.</p>
<p>Why does it contain duplicate sites (yellow) and proteins (cyan)?</p>
<p><a href="https://i.sstatic.net/BujcG.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/BujcG.png" alt="enter image description here" /></a></p>
<blockquote>
<p><em>Source data</em></p>
<p><a href="http://ftp.ebi.ac.uk/pride-archive/2020/12/PXD020517/MaxQuant_BA39_SOLUBLE.zip" rel="nofollow noreferrer">http://ftp.ebi.ac.uk/pride-archive/2020/12/PXD020517/MaxQuant_BA39_SOLUBLE.zip</a></p>
</blockquote>

<proteins><mass-spectrometry><maxquant>
Why does this modification site file contain duplicate sites and multiple related proteins?
# Why does this modification site file contain duplicate sites and multiple related proteins?

(Asked by: username_0 on 2022-03-04)

The data below is coming from a **MaxQuant** post-translational protein modification (PTM) site file.

Why does it contain duplicate sites (yellow) and proteins (cyan)?

[![enter image description here](https://i.sstatic.net/BujcG.png)](https://i.sstatic.net/BujcG.png)

> *Source data*
>
> <http://ftp.ebi.ac.uk/pride-archive/2020/12/PXD020517/MaxQuant_BA39_SOLUBLE.zip>

**Tags:** proteins, mass-spectrometry, maxquant

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## 2 answers

### Answer by username_1 on 2022-12-11. Score: 2

There are multiple protein isoforms that the gene *may* encode. The hyphen-number after the Uniprot ID represents the isoform —in a Uniprot you find the detail of these at the bottom.
The canonical isoform in Uniprot is the most likely one to be biologically relevant, while in NCBI and Ensembl it is the longest.
In a limited amount of case multiple isoforms are biologically relevant.
For the sake of sanity most variant annotation tools have a `canonical` argument to use the canonical.


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### Answer by username_0 on 2022-07-13. Score: 1

According to a proteomics researcher at the NIH:

* `proteins` column contains uniprot IDs.
* `position within proteins` column are the starting position of each ID.
* `position` is the *leading* protein


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