Proteome scale absolute quantification is fundamental for the quantitative 
understanding of an organism. The unsatisfactory accuracy for protein abundance 
estimation of current algorithms has been partially improved by the Absolute 
Protein EXpression profiling (APEX) algorithm, which implements the prior 
expectations of peptides' appearances in the calculation of protein abundances. 
However, the abundance feature (AF) in APEX is the spectral count (SC); an AF 
suffers from a narrow dynamic range, thus, unsatisfactory accuracy. Therefore, 
we adopted another tandem mass spectrometric (MS/MS) level AF called Summed 
MS/MS Total ion current (SMT), which cumulates the MS/MS fragment intensities 
rather than simply counting the MS/MS spectra, to surmount this particular 
deficiency. The combination of APEX and SMT (abbreviated as APEX-SMT) is capable 
of improving the accuracy of absolute quantification by reducing the average 
relative deviation by ~55-85% compared to that of APEX, through a series of 
tests on the Universal Proteomics Standard sample with a dynamic range of 5 
orders of magnitude (UPS2). The algorithm could also be used for relative 
quantification. When applied to the relative quantification of a publicly 
available benchmark dataset, APEX-SMT could provide comparable accuracy to APEX. 
All these results suggest that APEX-SMT is a promising alternative to APEX for 
proteome quantification.