Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function, urging the need for accurate cysteine oxidation quantification to decode protein redox regulation. Here, we present a novel approach called CysQuant that enables simultaneous quantification of cysteine oxidation degrees and protein abundancies. Reduced and reversibly oxidized cysteines are differentially labeled with light and heavy iodoacetamide isotopologues and analyzed using data-dependent acquisition (DDA) or data-independent acquisition (DIA) mass spectrometry. Using in silico predicted spectral libraries, plexDIA quantified on average 18% oxidized in the model plant Arabidopsis thaliana, though revealed a subset of highly oxidized cysteines part of disulfide bridges in AlphaFold2 predicted protein structures. Studying protein redox regulation of plant seedlings in response to excessive light, CysQuant successfully identified the well-established increased reduction of Calvin-Benson cycle enzymes, in addition to discovery of other, yet uncharacterized redox-sensitive disulfides in plastidial enzymes. CysQuant is widely applicable to diverse mass spectrometry platforms studying the cysteine modification status.