I need to do Mass spectrometry of my bovine intestine sample for analyzing proteome of host and microbial specific proteins and peptides.
I m unable to figure out whether software like maxquant can arrange by raw MS data based on their origin species. For ex- If I have GABÀ, will i know if its produced by host or the bacteria.
Can we do this kind of differentiation or I have to run MS for microbiome and host separately.
Kindly comment if anyone have an idea or can recommend any software that can perform this operation after obtaining raw MS data
Thanks
Hi Himani,
If you know which organisms are included in your samples you can work with a joined database fused from downloaded fasta format databases (i.e. from Uniprot) of the respective organisms.
With Maxquant you can than look at the number of unique/razor peptides to check from which organisms the proteins are more likely.
Best,
Murat
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