Label-free Quantification - Matching Corresponding Peptides

Matching Corresponding Peptides

In contrast to differential labelling, every biological specimen needs to be measured separately in a label-free experiment. The extracted peptide signals are then mapped across few or multiple LC-MS measurements using their coordinates on the mass-to-charge and retention-time dimensions. Data from high mass precision instruments greatly facilitate this process and increase the certainty of matching correct peptide signals across runs.

Clearly, differential processing of biological samples makes it necessary to have a standard which can be used to adjust the results. Peptides that are not expected to change in their expression levels in different biological samples may be used for this purpose. 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.