<p>Enhanced in-source fragmentation annotation combined with single quadrupole multiple reaction monitoring (EISA-MRM) has been designed for quantitative mass spectrometry analysis. EISA contrasts to traditional electrospray as a soft ionization technology and is proving to be advantageous since the resulting fragment ions are identical as those generated in tandem mass spectrometry. Criteria established by the European Union Commission Directive 2002/657/EC for electron ionization single quadrupole quantitative analysis was used for the EISA-MRM quantitative analyses and experiments were performed on multiple types of complex samples that included a mixture of 50 standards, as well as cell and plasma extracts. The dynamic range for quantitative analysis was comparable to QqQ-MRM analyses at up to 5 orders of magnitude and the EISA-MRM and QqQ-MRM of the cell and plasma extracts showed similar matrix effects. Amino acid and fatty acid measurements performed from certified NIST 1950 plasma with isotopically labelled standards demonstrated EISA-MRM accuracy in the range of 91-110% for the amino acids, 76-129% for the fatty acids, and precision with a CV < 10%. In order to enhance specificity and sensitivity, a newly developed Correlated SIM Chromatogram (CSC) algorithm was designed to facilitate MRM quality analyses. The EISA-MRM quantitative analysis with CSC informatics enables both precursor and in-source fragment ions to be correlated within a single quadrupole mass spectrometer.</p>