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. Author manuscript; available in PMC: 2016 Mar 3.
Published in final edited form as: Anal Chem. 2015 Feb 11;87(5):2570–2575. doi: 10.1021/ac503593d

Figure 2.

Figure 2

NeuCoDIA (MS2 quantification) generates fragment ion extracted ion chromatograms (XICs) that are comparable to those attained for the same parent ions using data-dependent acquisition (MS1 quantification): (A) MS1 spectra (240k resolution) attained during data-dependent analysis of the 10:1 yeast mixed-ratio sample and averaged over the 24 s that the peptides NIDNDFVEK2+ and ELYNNAHVYARDLK3+ were eluting. XICs reflect MS1 precursor ion intensities for NeuCode pairs over time (5-point boxcar average). (B) MS2 spectra (120k resolution, 27 Th isolation window centered on m/z 562.5) attained during NeuCoDIA analysis of the 10:1 yeast mixed-ratio sample and averaged over the 24 s that the precursors in part a (NIDNDFVEK2+ and ELYNNAHVYARDLK3+) were eluting. XICs reflect MS2 fragment ion intensities for fragment ion pairs over time (5-point boxcar average).