Hi, I would like to know some software and tools to analyze the M/Z data to identify the list of proteins that are obtained from ESI-MS. Along, could someone help me to calculate the score and sequence coverage of the proteins?
If you want to use a free available software I would recommend MaxQuant and Perseus. You can even find tutorials for both programmes on youtube, as the MaxQuant summer school is recorded every year.
The open-source software MaxQuant from the platform Perseus is commonly used to treat proteins metabolomics datasets but you could also use MZmine associated with your personal library massbank, or even OpenMS which has some ready-made tools for proteomics analyses.