High quality protein identification as well as accurate relative protein quantitation is done by nanoLC-MSMS. Reversed phase nano LC (Proxeon) using home made capillary columns results in peptide separations with a high resolution. MS spectra of the peptides are measured with an Orbitrap XL at approximately 5 ppm deviation or less. At the same time, MSMS spectra of the peptides are acquired in the LTQ. All measurements combined yield optimal protein identifications and relative quantitation.