While much attention in recent years has focused on genomic and transcriptomic biomarkers, these fail to capture the full phenotypic complexity of what’s going on within the body. Proteomics opens a window deep into this biology, revealing what happens at a molecular level during the development of disease or in response to treatment.

In this white paper, we walk through the two main strategies for collecting and analyzing mass spectrometry data for discovery proteomics using a label-free quantification (LFQ) approach: data-dependent and data-independent acquisition-based strategies. We discuss the advantages of each in different situations to help you apply the right method for your needs.