Label-free quantification is the quantification of MS peptide signals in LC/MS/MS data without an isotopic labeling reagent. Label-free quantification uses the Minora algorithm to perform untargeted feature detection, and it does not require an identification to quantify a peptide or protein. In theory, label-free quantification quantifies the most peptides and provides the widest dynamic range for untargeted workflows. It requires only a single PSM to quantify across all samples when you use retention-time alignment and feature mapping.

Label-free quantification proceeds as follows:

  1. First, the algorithm detects LC/MS peaks in the individual raw data files and maps them to identified PSMs, when available.
  2. Next, it creates new features from peaks that were not previously associated with any other feature. It takes all LC/MS peaks within a small retention-time range and checks for peaks that build isotope patterns.