Dear Esperanza,

If you are analyzing proteins from bovine samples you can either run Maxquant without including the contaminants list from Maxquant (by disabling teh include contaminants button in Maxquant's "Global parameters"/ "Sequences" tab.

You can also leave the contaminants + in your Perseus analysis if you dont filter them out.

If you want to have a contaminants fasta, containing only contaminants which are true contaminants for your experiments (all entries in the Maxquant contaminants list, except the bovine entries) you can open the contaminants fasta file of Maxquant, which is in the MaxQuant > bin > conf folder with WordPad (or any other suitable text editor) delete all bovine entries and save the file to have your own customized contaminants fasta file. I would recommend to keep a Copy of the original contaminants file in another folder (or by changing the name to i.e "MQcontaminants".

I guess you are doing analysis of protein corona of nanoparticles?

Best,

Murat

Dear Murat Eravci , thank you very much for your reply.

Yes, I am analyzing the protein corona. I did not know the contaminants could be customized based on your experiment (I thought it was something established). In that case, it is really useful to modify the contaminants fasta file of Maxquant.

Thank you.

Espe.

Hi Esperanza,

you are very welcome!

Are you doing your quantification with the Top3 method?

By the way,

I have attached a contaminants fasta file (see below) from which I have deleted all bovine entries as mentioned earlier. If you replace this file with the origianl file in your MQ conf folder, MQ will take this fasta for contaminants screening.

Best,

Murat