Thanks for your so fast answer. Moreover, could you tell me the meanings of "MS/MS count" and "reverse" columns in the output of MaxQuant?
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MaxQuant LFQ data cleanup
Hi all,
I am new to the proteomics data. A little confused about the LFQ data from MaxQuant software. Take some rows as examples tr|A0A087X106|A0A087X106_HUMAN;sp|O43790|KRT86_HUMAN;CON__O43790;sp|Q14533|KRT81_HUMAN;CON__Q14533 , what is the meaning of "tr" and "sp"?
In addition, I have been retrieving GENE IDs (e.g., A0A087X106, Q14533) with Uniprot accession IDs at Uniprot.org website. But many missings came out. Here I want to know any ideas to reduce the number of missings.
Thanks.
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You can find information on the FASTA header used by uniprot on the uniprot site.
db is ‘sp’ for UniProtKB/Swiss-Prot and ‘tr’ for UniProtKB/TrEMBL.
Regarding missing IDs, you'd need to post a few of them.
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I suspect this is in the Maxquant documentation, have a look there.
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