{{main|kapiler elektroforez–kütle spektrometrisi}}Kapiler elektroforez–kütle spektrometrisi (Capillary electrophoresis–mass spectrometry (CE-MS)) kapiler elektroforezin sıvı ayırma işlemini MS ile kombine eden bir tekniktir.<ref name="pmid2774189">{{cite journal|vauthors=Loo JA, Udseth HR, Smith RD|title=Peptide and protein analysis by electrospray ionization-mass spectrometry and capillary electrophoresis-mass spectrometry|journal=Analytical Biochemistry|volume=179|issue=2|pages=404–12|date=June 1989|pmid=2774189|doi=10.1016/0003-2697(89)90153-X}}</ref> CE-MS genellikle ESI ile kombine edilir.<ref name="pmid18790125">{{cite journal|vauthors=Maxwell EJ, Chen DD|title=Twenty years of interface development for capillary electrophoresis-electrospray ionization-mass spectrometry|journal=Analytica Chimica Acta|volume=627|issue=1|pages=25–33|date=October 2008|pmid=18790125|doi=10.1016/j.aca.2008.06.034|url=http://linkinghub.elsevier.com/retrieve/pii/S0003-2670(08)01244-0}}</ref>
