Light contamination in stable isotope-labelled internal peptide standards is frequent and a potential source of false discovery and quantitation error in proteomics

In mass spectrometry-based proteomics, heavy internal standards are used to validate target peptide detections and to calibrate peptide quantitation. Here, we report light contamination present in heavy labelled synthetic peptides of high isotopic enrichment. Application of such peptides as assay-internal standards potentially compromises the detection and quantitation especially of low abundant cellular peptides. Therefore, it is important to adopt guidelines to prevent false-positive identifications of endogenous light peptides as well as errors in their quantitation from biological samples.

Automated summary

In mass spectrometry-based proteomics, heavy internal standards are used for validating target peptide detections and calibrating peptide quantitation. However, contamination in heavy labelled synthetic peptides may compromise the detection and quantitation of low abundant cellular peptides. It is important to establish guidelines to prevent false-positive identifications of endogenous light peptides and errors in their quantitation from biological samples.