Response of peptide intensity to concentration in ESI-MS-based proteome

High-throughput quantification with label-free methods has received considerable attention in electrospray ionization (ESI)-mass spectrometry (MS), but the manner by which MS signals respond to peptide concentration remains unclear in proteomics. We developed a new mathematical formula to describe the intrinsic log-log relationship between the MS intensity response and peptide concentration in an analytical ESI process. Experimental results showed that the calibration curve is fairly fit to the log-log formula with a linear dynamic range of approximate four to five orders of magnitude. However, we found that the ionization of analytical peptides can be severely suppressed by coexisting matrix peptides, such that the calibration curve can be poorly leveled off on both ends. Our study suggests that the interferences from coexisting matrix peptides should be reduced in the ESI process to use the log-log calibration curve successfully for the high-throughput quantification.