How to import UniProt ID in Perseus?

Question

[hein]

Hi all,

Today I started with Perseus and received a proteomics Perseus dataset from my collaborator. When I tried to annotate GO terms, I realized my dataset is missing Uniprot IDs. Instead I have a column GENE (eg PRAM) or protein names in this format (sp|Q96QH2|PRAM_HUMAN). Is there an easy way to import UniProt IDs in this dataset?

Thanks!

[GenoMax]

We generally don't see a lot of activity on proteomics data front on biostars. You may want to ask this question directly in Perseus google group while you wait for a response here.

Answer 1

[majdabdu]

You probably already solved this, but here is how I would do it in Perseus version 1.6.6.0 in case someone else is wondering:

First, you need to make sure you download the annotations for your gene of interest. If you go to the Perseus directory on your computer, specifically to Perseus/bin/conf/annotations, do you have a txt.gz file for your organism of interest? For example: "mainAnnot.homo_sapiens.txt.gz" for human. If not, here is how to download it: From the main taskbar (at the top of the window), click Tools --> Annotation download, and follow the instructions.

Once you have the annotations file in the Perseus/bin/conf/annotations folder, you can get the UniProt identifiers as follows (you might need to restart your Perseus session): Annot. Columns --> To base identifiers For 'Identifiers', select the column the has your gene names/symbols For Identifier type' select the type of identifier you currently have (e.g. PRAM would be 'Gene name') Then hit OK.

You should get a new matrix with a new column that has the UniProt identifiers.