The authors would like to acknowledge Valentina Gelfanova for helpful suggestions regarding relative protein quantification and Dr.
Hale, "Comprehensive label-free method for the relative quantification of proteins from biological samples," Journal of Proteome Research, vol.
Mann, "MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification," Nature Biotechnology, vol.
A final approach to the identification of the application-specific requirements consists of the use of a pre-established checklist of quantification principles.
A second limitation of the present approach is that it does not lead to a unique quantification of the job worths.
As a byproduct of solving the latter problem, a unique quantification of the worths would be obtained, thereby indicating in what way the present biased evaluation needs correction.
Multiplexing for purposes of protein quantification is the ability to quantify multiple proteins during a single MS analysis (41-44).
In this investigation the quantification showed good reproducibility (CVs of 2%-22% in 10 runs, with more than three-quarters of the proteins showing CVs <10%).
As stated by the authors, with the imminent enhancements in mass spectrometers themselves, lower LOQs should be possible, and MRM-MS should be expandable for rapid, multiplexed quantification of 100 or more proteins in plasma.
Points of Concern for MRM-Based Protein Quantification
MRM-based quantification relies heavily on the monitoring of selected "proteotypic" peptides, or peptides that are precise and highly reproducible representations of the intact protein of interest, and their product ions (Fig.
Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in single-quandrupole ion trap.