What is the format of the protein list use for normalization

MannLabs / directlfq

Fast and accurate label-free quantification for small and very large numbers of proteomes

https://doi.org/10.1101/2023.02.17.528962

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What is the format of the protein list use for normalization #33

Closed Lang5991 closed 5 months ago

Lang5991 commented 5 months ago

Dear Mann, May I know what is the format of the protein list use for normalization?

Thanks

ammarcsj commented 5 months ago

Hi, you can just save a list like below as a file, e.g. with a .tsv or .txt ending.

PROTEIN_1 PROTEIN_2 .. PROTEIN_N

Lang5991 commented 5 months ago

Hi, you can just save a list like below as a file, e.g. with a .tsv or .txt ending.

PROTEIN_1 PROTEIN_2 .. PROTEIN_N

PROTEIN_1 means protein name(e.g. GAPDH), gene name(gapdh), or Uniprot_ID (e.g. Q5XJ10)? Thank you for your reply.

ammarcsj commented 5 months ago

The uniprot identifier.

Just to give some context: directLFQ per default uses the protein identifiers of the respective search engine outputs. With the list you specify which of those you want to use for normalization.