If you need more precise relative quantification of your proteins, we use a program called Pinnacle.
Pinnacle mines your raw data and extracts high-resolution MS1 protein quantification values that are very useful for more precise protein quantities used in time course studies, phosphorylation dynamics, or any experiment in which dynamic changes are expected.
As there is no free viewer for Pinnacle, you will receive your data in an Excel sheet as a simple list of protein & amount (or peptide/PTM & amount) for each sample.
Add $50/sample for Pinnacle.