MaxQuant LFQ data cleanup

Question

[boymin2020]

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.

Answer 1

[Devon Ryan]

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.

[boymin2020]

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?

[Devon Ryan]

I suspect this is in the Maxquant documentation, have a look there.