Fig. 2: Precision, accuracy, and utility of experimental peptide CCS values. | Nature Communications

Fig. 2: Precision, accuracy, and utility of experimental peptide CCS values.

From: Deep learning the collisional cross sections of the peptide universe from a million experimental values

Fig. 2

a Color-coded pairwise Pearson correlation values of peptide retention time (upper triangular matrix) and CCS values (lower triangular matrix) between the 168 LC-MS/MS runs of fractionated tryptic digests. Experimental metadata are indicated below the x-axis. White (n/a) indicates less than 5 data points for pairwise comparison. b CCS values of shared tryptic peptides independently measured in two typical LC-MS runs of fractions from Drosophila and HeLa (n = 68). c CVs of repeatedly measured peptide CCS values in the full dataset (n = 347,885 peptides). d Specificity of combined peptide m/z and CCS information for doubly and triply charged peptides with C-terminal arginine or lysine (n = 324,246 and 112,015) with a fixed m/z tolerance of ±1.5 ppm and as a function of CCS tolerance. For details, see main text and Methods.

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