Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics

J Proteome Res. 2020 Mar 6;19(3):1147-1153. doi: 10.1021/acs.jproteome.9b00666. Epub 2020 Feb 24.

Abstract

Mass spectrometry is a powerful tool for quantifying protein abundance in complex samples. Advances in sample preparation and the development of data-independent acquisition (DIA) mass spectrometry approaches have increased the number of peptides and proteins measured per sample. Here, we present a series of experiments demonstrating how to assess whether a peptide measurement is quantitative by mass spectrometry. Our results demonstrate that increasing the number of detected peptides in a proteomics experiment does not necessarily result in increased numbers of peptides that can be measured quantitatively.

Keywords: calibration curve; figures of merit; label-free quantification; mass spectrometry; quantitative proteomics.

Publication types

  • Research Support, N.I.H., Extramural