Discovery Proteomics and Absolute Protein Quantification Can Be Performed Simultaneously on an Orbitrap-Based Mass Spectrometer

[Image: see text] Mass spectrometry (MS) has steadily moved into the forefront of quantification-centered protein research. Protein cleavage isotope dilution MS is a proven way for quantifying proteins by using an isotope-labeled analogue of a peptide fragment of the parent protein as an internal standard. Parallel reaction monitoring (PRM) has become the go-to approach for such quantification on an Orbitrap-based instrument as it is assumed that the instrument sensitivity is enhanced. We performed a comparative study on data-dependent acquisition (DDA) and PRM-based workflows to quantify egg yolk protein precursors or vitellogenins (VTGs) Aa, Ab, and C in striped bass (Morone saxatilis). VTG proportions serve as a developmental measure of egg quality, possibly changing with the environment, and have been studied as an indicator of the health of North Carolina stocks. Based on single-factor analysis of variance comparisons of mean VTG amounts across fish from the same sample groupings, our results indicate that there is no statistical difference between MS1-based and MS2-based VTG quantification. We further conclude that DDA is able to deliver both discovery data and absolute quantification data in the same experiment.