Label-free quantification

Label-free quantification is a method in mass spectrometry that aims to determine the relative amount of proteins in two or more biological samples.

Spectral counting has problems due to the fact that the peptides are identified, thus making it necessary to run an additional MS/MS scan which takes time and therefore reduces the resolution of the experiment.

Data from high mass precision instruments greatly facilitate this process and increase the certainty of matching correct peptide signals across runs.

However, not all peptides ionize well and therefore the choice of candidates should be done after an initial study which should only characterize the protein content of the biological samples that will be investigated.

Finally, sophisticated normalization methods are used to remove systematic artefacts in the peptide intensity values between LC-MS measurements.

Label-free quantification experiment with 3 samples, 3 LC-MS files and 5 precursor ions/peptides. Intensities at the peak of the chromatographic peaks are used for quantification in this particular case. Peptides are identified via fragmentation mass spectra, and some of the precursor ions will be quantified, but not mapped to any peptide sequence.