Hi, 

To get proper help you certainly need to provide more information , 

- what is your sample ?

-lc ms system ?

-ms method ? 

- goal of analysis ? 

Etc 

Cheers h 

Thanks Hendrik

My goal is to look for the differentially expressed proteins in diseased tissues.

But for different lc ms system there is various softwares for data analysis. You need to be really specific- thats the way how the proteomics works :) And what information you want to obtain about quantities, PTMs, or...

create account with XCMS online. Convert your files to mxXML format using MSconvert. Upload your files to the server and perform you analysis. You will get a diff report of your two cohorts with differential comparison. Further apply statistical analysis to your data to reduce them into your top proteins of interest. Apply p value and fold change filters to reduce your targets to those which are showing potential biomarkers.