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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)?

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Source data

http://ftp.ebi.ac.uk/pride-archive/2020/12/PXD020517/MaxQuant_BA39_SOLUBLE.zip

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2 Answers 2

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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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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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