A peptide‐centric approach to breast cancer biomarker discovery utilizing label‐free multiple reaction monitoring mass spectrometry

<jats:title>Abstract</jats:title><jats:p>We report an approach for multiplex analysis of cancer biomarkers based on the measurement of diagnostic peptides in whole tissue protein digests. Label‐free quantitation with MS3 multiple reaction monitoring (MRM) was developed to afford accurate analysis of prospective marker peptides in a panel of breast tumors. This approach provides an economical and robust alternative to stable isotope‐based methods. It is equally applicable to the analysis of samples derived from tissue biopsy, aspirate, or plasma and can be easily translated to clinic.</jats:p>